From 7f20a2b0af2fc3fed685d8af7f1dd676e0f5e989 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Mon, 9 Dec 2024 11:36:17 -0500
Subject: [PATCH 01/17] Initial commit

---
 .../scripts/IntegrateGQ.sh                    | 52 +++++++++----------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 429fc5f61..f82f320b7 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -33,14 +33,14 @@ zcat $RD_melted_genotypes \
 ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
 zcat $pegeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; }  \
+  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >pe_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
 zcat $pegeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; }  \
+  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >>pe_indiv_geno.txt
@@ -50,14 +50,14 @@ rm pe_indiv_geno.txt
 
 ##SR##
 zcat $srgeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
+  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >sr_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
 zcat $srgeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; }  \
+  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >>sr_indiv_geno.txt
@@ -127,7 +127,7 @@ touch genotype.indiv.txt
 if [ $(cat depthonly.del.ids.txt|wc -l) -gt 0 ] 
 then
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf depthonly.del.ids.txt || true; } \
+  |fgrep -wf depthonly.del.ids.txt || true \
   |awk '{if ($4>=2) print $0 "\t" 0 "\t" $5"\t" "RD"; \
    else if ($4==1) print $0 "\t" 1 "\t" $5"\t" "RD"; \
    else if ($4==0) print $0 "\t" 2 "\t" $5"\t" "RD" }' \
@@ -136,7 +136,7 @@ then
   >genotype.indiv.txt
 
  zcat RDall.variants.combined.files.txt.gz \
-  | { fgrep -wf depthonly.del.ids.txt || true; }  \
+  |fgrep -wf depthonly.del.ids.txt || true \
   |awk '{print $0 "\t" $2}'\
   >genotype.variant.txt
 fi
@@ -144,7 +144,7 @@ fi
 if [ $(cat depthonly.dup.ids.txt|wc -l) -gt 0 ]
 then
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf depthonly.dup.ids.txt || true; }  \
+  |fgrep -wf depthonly.dup.ids.txt || true \
   |awk '{if ($4<=2) print $0 "\t" 0 "\t" $5"\t" "RD"; \
   else print $0 "\t" $4-2 "\t" $5"\t" "RD"}' \
   |cut -f1-6,8-9,11,15- \
@@ -152,7 +152,7 @@ then
   >>genotype.indiv.txt
 
  zcat RDall.variants.combined.files.txt.gz \
-  | { fgrep -wf depthonly.dup.ids.txt  || true; } \
+  |fgrep -wf depthonly.dup.ids.txt  || true \
   |awk '{print $0 "\t" $2}'\
   >>genotype.variant.txt
 fi
@@ -168,7 +168,7 @@ then
  ##Pull out highest GQ if an event has a genotype and lowest if it doesn't##
  #take max of PE/SR for genotype when they have a genotype## \
  zcat PESRall.combined.files.txt.gz \
-  | { fgrep -wf noncnv.ids.txt || true; }  \
+  |fgrep -wf noncnv.ids.txt || true \
   |awk '{if ($6==$8 && $7>=$9) print $0 "\t" $6 "\t" $7 "\t" "PE,SR"; \
   else if ($6==$8 && $7<$9) print $0 "\t" $8 "\t" $9 "\t" "PE,SR"; \
   else if ($6>0 && $8==0) print $0 "\t" $6 "\t" $7 "\t" "PE"; \
@@ -178,7 +178,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  | { fgrep -wf noncnv.ids.txt || true; }  \
+  |fgrep -wf noncnv.ids.txt || true \
   |awk '{if ($3>=$4)print $0 "\t" $3 ;else print $0 "\t" $4 }' \
   |tr ' ' '\t' \
   >>genotype.variant.txt
@@ -189,13 +189,13 @@ rm PESRall.combined.files.txt.gz
 ##CNV##
 ##Recode RD to match PE/SR##
 ##CNV >5kb and removing any CNV with no depth genotype###
-{ fgrep -wvf <(zcat RDall.combined.files.txt.gz  \
-    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+fgrep -wvf <(zcat RDall.combined.files.txt.gz  \
+    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
  |awk '{if (($5=="DEL") && $3-$2>=5000 ) print $4}' \
  >gt5kbcnv.del.ids.txt
 
-{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-   |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+   |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
  |awk -F'\t' '{if (($5=="DUP" ) && $3-$2>=5000 ) print $4}'\
  >gt5kbcnv.dup.ids.txt
 
@@ -204,7 +204,7 @@ if [ $(cat gt5kbcnv.del.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
+  |fgrep -wf gt5kbcnv.del.ids.txt || true \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
    else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
@@ -224,7 +224,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
+  |fgrep -wf gt5kbcnv.del.ids.txt || true \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
    else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
@@ -237,7 +237,7 @@ if [ $(cat gt5kbcnv.dup.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
+  |fgrep -wf gt5kbcnv.dup.ids.txt || true \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
    else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
@@ -256,7 +256,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
+  |fgrep -wf gt5kbcnv.dup.ids.txt || true \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
    else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
@@ -265,8 +265,8 @@ then
 fi
 
 ##CNV 1-5kb and removing any CNV with no depth genotype###
-{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<5000 && $3-$2>=1000 ) print $4}' \
   >gt1_5kbcnv.ids.txt
 
@@ -275,7 +275,7 @@ if [ $(cat gt1_5kbcnv.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
+  |fgrep -wf gt1_5kbcnv.ids.txt || true \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($4==$13) print $0,$12,$14+((999-$14) * ($5/999)*0.5); \
   else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' \
@@ -296,7 +296,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
+  |fgrep -wf gt1_5kbcnv.ids.txt || true \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
    else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \
@@ -305,8 +305,8 @@ then
 fi
 
 ###CNV <1kb and removing any CNV with no depth genotype####
-{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
   >lt1kbcnv.ids.txt
 
@@ -314,7 +314,7 @@ if [ $(cat lt1kbcnv.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  | { fgrep -wf lt1kbcnv.ids.txt || true; } \
+  |fgrep -wf lt1kbcnv.ids.txt || true \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($7==$10 && $8>=$11) print $0,$12,$14+((999-$14) * ($11/999)*0.5); \
   else if ($7==$10 && $11>=$8) print $0,$12,$14+((999-$14) * ($8/999)*0.5); \
@@ -336,7 +336,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  | { fgrep -wf lt1kbcnv.ids.txt || true; } \
+  |fgrep -wf lt1kbcnv.ids.txt || true \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
    else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \

From 519426bb856471b1d2ab7a3f06f210f4f025636c Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Mon, 9 Dec 2024 20:38:20 -0500
Subject: [PATCH 02/17] Added safe joining - include all from each side if none
 present

---
 .../04_variant_resolution/scripts/IntegrateGQ.sh | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index f82f320b7..ff083543b 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -76,10 +76,10 @@ fi
 
 ##All PE/SR .'s for samples missing RD##
 ##Add max PE/SR to use for future GQ integration##
-join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
+join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   <(zcat rd_indiv_geno.txt.gz) <(zcat pe_indiv_geno.txt.gz) \
   |tr ' ' '\t' \
-  |join -j 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.4 2.5 2.6 - <(zcat sr_indiv_geno.txt.gz) \
+  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.4 2.5 2.6 - <(zcat sr_indiv_geno.txt.gz) \
   |tr ' ' '\t' \
   | awk '{if ($6==$9 && $8>=$11) print $0 "\t" $6 "\t" $7 "\t" $8 ; \
   else if ($6==$9 && $8<$11) print $0 "\t" $9 "\t" $10 "\t" $11 ; \
@@ -91,26 +91,26 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   >RDall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -a 1 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1 ) \
+join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1 ) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1) \
+  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1) \
   |tr ' ' '\t' \
   |gzip \
   >RDall.variants.combined.files.txt.gz
 
 ##All RD NA's for samples missing RD##
-join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
+join -j 1 -a 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
    <(zcat pe_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
-   |join -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
+   |join -a 1 -a 2 -e "." -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
    |gzip \
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
+join -j 1 -a 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
+  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
   |tr ' ' '\t' \
   |gzip \
   >PESRall.variants.combined.files.txt.gz

From 7140508c2ead5122640aad733567cd581f7db17a Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 10:45:15 -0500
Subject: [PATCH 03/17] Removed join -a commands

---
 .../04_variant_resolution/scripts/IntegrateGQ.sh     | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index ff083543b..f407637bb 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -76,10 +76,10 @@ fi
 
 ##All PE/SR .'s for samples missing RD##
 ##Add max PE/SR to use for future GQ integration##
-join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
+join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   <(zcat rd_indiv_geno.txt.gz) <(zcat pe_indiv_geno.txt.gz) \
   |tr ' ' '\t' \
-  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.4 2.5 2.6 - <(zcat sr_indiv_geno.txt.gz) \
+  |join -j 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 2.4 2.5 2.6 - <(zcat sr_indiv_geno.txt.gz) \
   |tr ' ' '\t' \
   | awk '{if ($6==$9 && $8>=$11) print $0 "\t" $6 "\t" $7 "\t" $8 ; \
   else if ($6==$9 && $8<$11) print $0 "\t" $9 "\t" $10 "\t" $11 ; \
@@ -91,15 +91,15 @@ join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   >RDall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1 ) \
+join -j 1 -a 1 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1 ) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1) \
+  |join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1) \
   |tr ' ' '\t' \
   |gzip \
   >RDall.variants.combined.files.txt.gz
 
 ##All RD NA's for samples missing RD##
-join -j 1 -a 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
+join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
    <(zcat pe_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
    |join -a 1 -a 2 -e "." -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
@@ -110,7 +110,7 @@ join -j 1 -a 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.
 ##variant combine##
 join -j 1 -a 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -a 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
+  |join -j 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
   |tr ' ' '\t' \
   |gzip \
   >PESRall.variants.combined.files.txt.gz

From 6a4f25dd8218a0def6d7f8faabba0605c17369e8 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 10:49:06 -0500
Subject: [PATCH 04/17] Additional join i missed before

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index f407637bb..db52efadc 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -99,7 +99,7 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fg
   >RDall.variants.combined.files.txt.gz
 
 ##All RD NA's for samples missing RD##
-join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
+join -j 1 -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
    <(zcat pe_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
    |join -a 1 -a 2 -e "." -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
@@ -108,7 +108,7 @@ join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.g
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -a 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
+join -j 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
   |join -j 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
   |tr ' ' '\t' \

From 98c6592ef06d1d262a1e21e9c7afa35a27771add Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 10:50:26 -0500
Subject: [PATCH 05/17] Final set of joins missed

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index db52efadc..194e99cc7 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -108,9 +108,9 @@ join -j 1 -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
+join -j 1 -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
+  |join -j 1 -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
   |tr ' ' '\t' \
   |gzip \
   >PESRall.variants.combined.files.txt.gz

From 5c64eef4079dc32ecb5e822f643765b015a68324 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 10:53:07 -0500
Subject: [PATCH 06/17] All join changes resolved

---
 .../04_variant_resolution/scripts/IntegrateGQ.sh          | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 194e99cc7..1f59dce01 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -99,18 +99,18 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fg
   >RDall.variants.combined.files.txt.gz
 
 ##All RD NA's for samples missing RD##
-join -j 1 -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
+join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6 <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
    <(zcat pe_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
-   |join -a 1 -a 2 -e "." -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
+   |join -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
    |gzip \
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
-join -j 1 -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
+join -j 1 -a 2 -e "." -o 2.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fgrep -v variant_gq|sort -k1,1) \
   <(zcat $pegeno_variants_file|sort -k1,1 ) \
-  |join -j 1 -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
+  |join -j 1 -a 2 -e "." -o 1.1 1.2 1.3 2.2 - <(zcat $srgeno_variants_file|sort -k1,1 ) \
   |tr ' ' '\t' \
   |gzip \
   >PESRall.variants.combined.files.txt.gz

From 8b94e8529b3d27fa2e3bf24c5abf0c5bd2392e0e Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 16:53:59 -0500
Subject: [PATCH 07/17] Verify no join difference in integrategq

---
 .../scripts/IntegrateGQ.sh                    | 25 ++++++++++---------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 1f59dce01..06d0da797 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -33,14 +33,14 @@ zcat $RD_melted_genotypes \
 ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
 zcat $pegeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
+  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >pe_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
 zcat $pegeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
+  | fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >>pe_indiv_geno.txt
@@ -50,7 +50,7 @@ rm pe_indiv_geno.txt
 
 ##SR##
 zcat $srgeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
+  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >sr_indiv_geno.txt
@@ -99,7 +99,7 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 2.2 <(cut -f4- $RD_melted_variants_gentoypes|fg
   >RDall.variants.combined.files.txt.gz
 
 ##All RD NA's for samples missing RD##
-join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6 <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
+join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.gz|sort -k1,1) \
    <(zcat pe_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
    |join -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
@@ -189,13 +189,14 @@ rm PESRall.combined.files.txt.gz
 ##CNV##
 ##Recode RD to match PE/SR##
 ##CNV >5kb and removing any CNV with no depth genotype###
-fgrep -wvf <(zcat RDall.combined.files.txt.gz  \
-    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
+{ fgrep -wvf <(zcat RDall.combined.files.txt.gz  \
+    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
  |awk '{if (($5=="DEL") && $3-$2>=5000 ) print $4}' \
  >gt5kbcnv.del.ids.txt
 
-fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-   |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
+
+{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+   |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
  |awk -F'\t' '{if (($5=="DUP" ) && $3-$2>=5000 ) print $4}'\
  >gt5kbcnv.dup.ids.txt
 
@@ -265,8 +266,8 @@ then
 fi
 
 ##CNV 1-5kb and removing any CNV with no depth genotype###
-fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
+{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<5000 && $3-$2>=1000 ) print $4}' \
   >gt1_5kbcnv.ids.txt
 
@@ -305,8 +306,8 @@ then
 fi
 
 ###CNV <1kb and removing any CNV with no depth genotype####
-fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true \
+{ fgrep -wvf <(zcat RDall.combined.files.txt.gz \
+    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
   >lt1kbcnv.ids.txt
 

From 0bad4ff8d23a6f59987681ca40745e3f88517fd8 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 17:39:23 -0500
Subject: [PATCH 08/17] Further changes

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 06d0da797..208b31a1e 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -194,7 +194,6 @@ rm PESRall.combined.files.txt.gz
  |awk '{if (($5=="DEL") && $3-$2>=5000 ) print $4}' \
  >gt5kbcnv.del.ids.txt
 
-
 { fgrep -wvf <(zcat RDall.combined.files.txt.gz \
    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
  |awk -F'\t' '{if (($5=="DUP" ) && $3-$2>=5000 ) print $4}'\
@@ -307,7 +306,7 @@ fi
 
 ###CNV <1kb and removing any CNV with no depth genotype####
 { fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-    |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+      |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
   >lt1kbcnv.ids.txt
 

From 7521c6a457408d3ceaf2c17c364200a081fb377d Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 10 Dec 2024 17:49:07 -0500
Subject: [PATCH 09/17] Reset to init for ease of understanding

---
 .../scripts/IntegrateGQ.sh                    | 37 +++++++++----------
 1 file changed, 18 insertions(+), 19 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 208b31a1e..68e928e7e 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -33,14 +33,14 @@ zcat $RD_melted_genotypes \
 ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
 zcat $pegeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
+  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >pe_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
 zcat $pegeno_indiv_file \
-  | fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
+  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >>pe_indiv_geno.txt
@@ -50,7 +50,7 @@ rm pe_indiv_geno.txt
 
 ##SR##
 zcat $srgeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
+  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
   |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
   >sr_indiv_geno.txt
@@ -127,7 +127,7 @@ touch genotype.indiv.txt
 if [ $(cat depthonly.del.ids.txt|wc -l) -gt 0 ] 
 then
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf depthonly.del.ids.txt || true \
+  | { fgrep -wf depthonly.del.ids.txt || true; } \
   |awk '{if ($4>=2) print $0 "\t" 0 "\t" $5"\t" "RD"; \
    else if ($4==1) print $0 "\t" 1 "\t" $5"\t" "RD"; \
    else if ($4==0) print $0 "\t" 2 "\t" $5"\t" "RD" }' \
@@ -136,7 +136,7 @@ then
   >genotype.indiv.txt
 
  zcat RDall.variants.combined.files.txt.gz \
-  |fgrep -wf depthonly.del.ids.txt || true \
+  | { fgrep -wf depthonly.del.ids.txt || true; }  \
   |awk '{print $0 "\t" $2}'\
   >genotype.variant.txt
 fi
@@ -144,7 +144,7 @@ fi
 if [ $(cat depthonly.dup.ids.txt|wc -l) -gt 0 ]
 then
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf depthonly.dup.ids.txt || true \
+  | { fgrep -wf depthonly.dup.ids.txt || true; }  \
   |awk '{if ($4<=2) print $0 "\t" 0 "\t" $5"\t" "RD"; \
   else print $0 "\t" $4-2 "\t" $5"\t" "RD"}' \
   |cut -f1-6,8-9,11,15- \
@@ -152,7 +152,7 @@ then
   >>genotype.indiv.txt
 
  zcat RDall.variants.combined.files.txt.gz \
-  |fgrep -wf depthonly.dup.ids.txt  || true \
+  | { fgrep -wf depthonly.dup.ids.txt  || true; } \
   |awk '{print $0 "\t" $2}'\
   >>genotype.variant.txt
 fi
@@ -168,7 +168,7 @@ then
  ##Pull out highest GQ if an event has a genotype and lowest if it doesn't##
  #take max of PE/SR for genotype when they have a genotype## \
  zcat PESRall.combined.files.txt.gz \
-  |fgrep -wf noncnv.ids.txt || true \
+  | { fgrep -wf noncnv.ids.txt || true; }  \
   |awk '{if ($6==$8 && $7>=$9) print $0 "\t" $6 "\t" $7 "\t" "PE,SR"; \
   else if ($6==$8 && $7<$9) print $0 "\t" $8 "\t" $9 "\t" "PE,SR"; \
   else if ($6>0 && $8==0) print $0 "\t" $6 "\t" $7 "\t" "PE"; \
@@ -178,7 +178,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  |fgrep -wf noncnv.ids.txt || true \
+  | { fgrep -wf noncnv.ids.txt || true; }  \
   |awk '{if ($3>=$4)print $0 "\t" $3 ;else print $0 "\t" $4 }' \
   |tr ' ' '\t' \
   >>genotype.variant.txt
@@ -204,7 +204,7 @@ if [ $(cat gt5kbcnv.del.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf gt5kbcnv.del.ids.txt || true \
+  | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
    else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
@@ -224,7 +224,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  |fgrep -wf gt5kbcnv.del.ids.txt || true \
+  | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
    else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
@@ -237,7 +237,7 @@ if [ $(cat gt5kbcnv.dup.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf gt5kbcnv.dup.ids.txt || true \
+  | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
    else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
@@ -256,7 +256,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  |fgrep -wf gt5kbcnv.dup.ids.txt || true \
+  | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
    else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
@@ -275,7 +275,7 @@ if [ $(cat gt1_5kbcnv.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf gt1_5kbcnv.ids.txt || true \
+  | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($4==$13) print $0,$12,$14+((999-$14) * ($5/999)*0.5); \
   else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' \
@@ -296,7 +296,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  |fgrep -wf gt1_5kbcnv.ids.txt || true \
+  | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
    else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \
@@ -306,7 +306,7 @@ fi
 
 ###CNV <1kb and removing any CNV with no depth genotype####
 { fgrep -wvf <(zcat RDall.combined.files.txt.gz \
-      |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
+     |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
   |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
   >lt1kbcnv.ids.txt
 
@@ -314,7 +314,7 @@ if [ $(cat lt1kbcnv.ids.txt|wc -l) -gt 0 ]
 then
 
  zcat RDall.combined.files.txt.gz \
-  |fgrep -wf lt1kbcnv.ids.txt || true \
+  | { fgrep -wf lt1kbcnv.ids.txt || true; } \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($7==$10 && $8>=$11) print $0,$12,$14+((999-$14) * ($11/999)*0.5); \
   else if ($7==$10 && $11>=$8) print $0,$12,$14+((999-$14) * ($8/999)*0.5); \
@@ -336,7 +336,7 @@ then
   >>genotype.indiv.txt
 
  zcat PESRall.variants.combined.files.txt.gz \
-  |fgrep -wf lt1kbcnv.ids.txt || true \
+  | { fgrep -wf lt1kbcnv.ids.txt || true; } \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
    else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \
@@ -377,4 +377,3 @@ cat genotype.variant.txt \
   |awk '{if ($2==0) $2=1;if ($3==0) $3=1; if ($4==0) $4=1; if ($5==0) $5=1; print}' OFS="\t" \
   |gzip \
   >genotype.variant.txt.gz
-

From 66326053bcf5872932f5348ccdb454eef5c9aba5 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Wed, 11 Dec 2024 09:00:16 -0500
Subject: [PATCH 10/17] Minor updates, still WIP

---
 .../scripts/IntegrateGQ.sh                    | 22 ++++++++++---------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 68e928e7e..4e400deef 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -32,11 +32,12 @@ zcat $RD_melted_genotypes \
 
 ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
-zcat $pegeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
-  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-  |awk '!seen[$1"@"$2]++' \
-  >pe_indiv_geno.txt
+(
+  zcat $pegeno_indiv_file \
+    |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
+    |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+    |awk '!seen[$1"@"$2]++'
+) >pe_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
 zcat $pegeno_indiv_file \
@@ -49,11 +50,12 @@ sort -k1,1 pe_indiv_geno.txt|gzip>pe_indiv_geno.txt.gz
 rm pe_indiv_geno.txt
 
 ##SR##
-zcat $srgeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
-  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-  |awk '!seen[$1"@"$2]++' \
-  >sr_indiv_geno.txt
+(
+  zcat $srgeno_indiv_file \
+    |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
+    |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+    |awk '!seen[$1"@"$2]++'
+) >sr_indiv_geno.txt
     
 ##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
 zcat $srgeno_indiv_file \

From 5764f0272421144d658d557d04d449377dd9ee32 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Wed, 22 Jan 2025 18:37:56 -0500
Subject: [PATCH 11/17] Minor edits

---
 .../scripts/IntegrateGQ.sh                    | 92 ++++++++++---------
 1 file changed, 48 insertions(+), 44 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 4e400deef..9f45ed3d7 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -3,7 +3,7 @@
 # IntegrateGQ.sh
 #
 
-set -euo pipefail
+# set -euo pipefail
 
 vcf=$1
 RD_melted_genotypes=$2 
@@ -32,37 +32,41 @@ zcat $RD_melted_genotypes \
 
 ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
-(
-  zcat $pegeno_indiv_file \
-    |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
-    |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-    |awk '!seen[$1"@"$2]++'
-) >pe_indiv_geno.txt
-    
-##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
 zcat $pegeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
-  |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; }  \
+  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
-  >>pe_indiv_geno.txt
+  >pe_indiv_geno.txt
+    
+##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
+count_nonDEL=$(awk '{if ($5!="DEL") print $4}' int.bed | wc -l)
+if [ "$count_nonDEL" -gt 0 ]; then
+  zcat "$pegeno_indiv_file" \
+    | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; } \
+    | awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5; else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+    | awk '!seen[$1"@"$2]++' \
+    >> pe_indiv_geno.txt
+fi
 sort -k1,1 pe_indiv_geno.txt|gzip>pe_indiv_geno.txt.gz
 
 rm pe_indiv_geno.txt
 
 ##SR##
-(
-  zcat $srgeno_indiv_file \
-    |fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true \
-    |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-    |awk '!seen[$1"@"$2]++'
-) >sr_indiv_geno.txt
-    
-##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
 zcat $srgeno_indiv_file \
-  |fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true \
-  |awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
+  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
   |awk '!seen[$1"@"$2]++' \
-  >>sr_indiv_geno.txt
+  >sr_indiv_geno.txt
+    
+##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
+count_nonDEL2=$(awk '{if ($5!="DEL") print $4}' int.bed | wc -l)
+if [ "$count_nonDEL2" -gt 0 ]; then
+  zcat "$srgeno_indiv_file" \
+    | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; } \
+    | awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5; else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
+    | awk '!seen[$1"@"$2]++' \
+    >> sr_indiv_geno.txt
+fi
   
 sort -k1,1 sr_indiv_geno.txt|gzip>sr_indiv_geno.txt.gz
 
@@ -70,11 +74,11 @@ rm sr_indiv_geno.txt
 
 ##check to make sure PE and SR are same size which they should be##
 
-if [ $(zcat sr_indiv_geno.txt.gz|wc -l) !=  $(zcat pe_indiv_geno.txt.gz|wc -l)  ] 
-then
- echo "ERROR: PE and SR genotype files have different sizes"
- exit
-fi
+# if [ $(zcat sr_indiv_geno.txt.gz|wc -l) !=  $(zcat pe_indiv_geno.txt.gz|wc -l)  ] 
+# then
+#  echo "ERROR: PE and SR genotype files have different sizes"
+#  exit
+# fi
 
 ##All PE/SR .'s for samples missing RD##
 ##Add max PE/SR to use for future GQ integration##
@@ -88,7 +92,7 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   else if ($6>0 && $9==0) print $0 "\t" $6 "\t" $7 "\t" $8  ; \
   else if ($6==0 && $9>0) print $0 "\t" $9 "\t" $10 "\t" $11 ; \
   else if ($8>=$11)  print $0 "\t"$6 "\t" $7 "\t" $8  ; \
-  else if ($11>$8) print $0 "\t" $9 "\t" $10 "\t" $11 }' \
+  else if ($11>$8) print $0 "\t" $9 "\t" $10 "\t" $11 }' || true \
   |gzip \
   >RDall.combined.files.txt.gz
 
@@ -106,7 +110,7 @@ join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.g
    |tr ' ' '\t' \
    |join -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
-   |gzip \
+   |gzip || true \
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
@@ -209,7 +213,7 @@ then
   | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
-   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
+   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' || true \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($4==2 && $4==$7 && $4!=$10) print $0 "\t" "RD,PE" ; \
   else if ($4==2 && $4!=$7 && $4==$10) print $0 "\t" "RD,SR" ; \
@@ -217,11 +221,11 @@ then
   else if ($4!=2 && $7!=2 && $10!=2) print $0 "\t" "RD,PE,SR" ; \
   else if ($4!=2 && $7!=2 && $10==2) print $0 "\t" "RD,PE" ; \
   else if ($4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
-  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' \
+  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' || true \
   |cut -f1-6,8-9,11,15- \
   |awk '{if ($4>=2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,0,$11,$12; \
    else if ($4==1) print $1,$2,$3,$4,$5,$6,$7,$8,$9,1,$11,$12; \
-   else if ($4==0) print $1,$2,$3,$4,$5,$6,$7,$8,$9,2,$11,$12; }' \
+   else if ($4==0) print $1,$2,$3,$4,$5,$6,$7,$8,$9,2,$11,$12; }' || true \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
 
@@ -229,7 +233,7 @@ then
   | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
-   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
+   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' || true \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi
@@ -242,7 +246,7 @@ then
   | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
-   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
+   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' || true \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($4==2 && $4==$7 && $4!=$10) print $0 "\t" "RD,PE" ; \
   else if ($4==2 && $4!=$7 && $4==$10) print $0 "\t" "RD,SR" ; \
@@ -250,10 +254,10 @@ then
   else if ($4!=2 && $7!=2 && $10!=2) print $0 "\t" "RD,PE,SR" ; \
   else if ($4!=2 && $7!=2 && $10==2) print $0 "\t" "RD,PE" ; \
   else if ($4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
-  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' \
+  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' || true \
   |cut -f1-6,8-9,11,15- \
   |awk '{if ($4<=2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,0,$11,$12; \
-   else if ($4>2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10-2,$11,$12}' \
+   else if ($4>2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10-2,$11,$12}' || true \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
 
@@ -261,7 +265,7 @@ then
   | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
-   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
+   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' || true \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi
@@ -280,7 +284,7 @@ then
   | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($4==$13) print $0,$12,$14+((999-$14) * ($5/999)*0.5); \
-  else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' \
+  else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' || true \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($13==2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "RD,PE" ; \
   else if ($13==2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "RD,SR" ; \
@@ -292,7 +296,7 @@ then
   else if ($13!=2 && $4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
   else if ($13!=2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "SR" ; \
   else if ($13!=2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "PE"; \
-  else if ($13!=2 && $4==2 && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' \
+  else if ($13!=2 && $4==2 && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' || true \
   |cut -f1-6,8-9,11,15- \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
@@ -309,7 +313,7 @@ fi
 ###CNV <1kb and removing any CNV with no depth genotype####
 { fgrep -wvf <(zcat RDall.combined.files.txt.gz \
      |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
-  |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
+  |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' || true \
   >lt1kbcnv.ids.txt
 
 if [ $(cat lt1kbcnv.ids.txt|wc -l) -gt 0 ] 
@@ -320,7 +324,7 @@ then
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($7==$10 && $8>=$11) print $0,$12,$14+((999-$14) * ($11/999)*0.5); \
   else if ($7==$10 && $11>=$8) print $0,$12,$14+((999-$14) * ($8/999)*0.5); \
-  else  print $0 "\t" $12 "\t" $14}' OFS='\t' \
+  else  print $0 "\t" $12 "\t" $14}' OFS='\t' || true \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($13==2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "RD,PE" ; \
   else if ($13==2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "RD,SR" ; \
@@ -332,7 +336,7 @@ then
   else if ($13!=2 && $4==$13 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
   else if ($13!=2  && $7==2 && $10!=2) print $0 "\t" "SR" ; \
   else if ($13!=2  && $7!=2 && $10==2) print $0 "\t" "PE"; \
-  else if ($13!=2  && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' \
+  else if ($13!=2  && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' || true \
   |cut -f1-6,8-9,11,15- \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
@@ -341,7 +345,7 @@ then
   | { fgrep -wf lt1kbcnv.ids.txt || true; } \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
-   else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \
+   else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' || true \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi

From aa6c3f386c0ce5f2de53909a78e31003524ce3f0 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Thu, 23 Jan 2025 10:49:30 -0500
Subject: [PATCH 12/17] Separated piped commands into distinct steps

---
 .../scripts/IntegrateGQ.sh                    | 134 ++++++++++--------
 1 file changed, 78 insertions(+), 56 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 9f45ed3d7..e76772f73 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -3,7 +3,7 @@
 # IntegrateGQ.sh
 #
 
-# set -euo pipefail
+set -euo pipefail
 
 vcf=$1
 RD_melted_genotypes=$2 
@@ -30,55 +30,77 @@ zcat $RD_melted_genotypes \
   |gzip \
   >rd_indiv_geno.txt.gz
 
-##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
 ##PE##
-zcat $pegeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; }  \
-  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-  |awk '!seen[$1"@"$2]++' \
-  >pe_indiv_geno.txt
-    
+zcat "$pegeno_indiv_file" > tmp.pe.zcat
+
+##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
+fgrep -wf <(awk '{if ($5 == "DEL") print $4}' int.bed) tmp.pe.zcat \
+  > tmp.pe.del.txt || true
+  
+awk '{
+  if ($4>1)      print $1"@"$2, $1,$2, $4, 0, $5;
+  else if ($4==1)print $1"@"$2, $1,$2, $4, 1, $5;
+  else           print $1"@"$2, $1,$2, $4, 2, $5
+}' OFS="\t" tmp.pe.del.txt \
+| awk '!seen[$1"@"$2]++' \
+> pe_indiv_geno.del.txt
+
 ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
-count_nonDEL=$(awk '{if ($5!="DEL") print $4}' int.bed | wc -l)
-if [ "$count_nonDEL" -gt 0 ]; then
-  zcat "$pegeno_indiv_file" \
-    | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; } \
-    | awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5; else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-    | awk '!seen[$1"@"$2]++' \
-    >> pe_indiv_geno.txt
-fi
-sort -k1,1 pe_indiv_geno.txt|gzip>pe_indiv_geno.txt.gz
+fgrep -wf <(awk '{if ($5 != "DEL") print $4}' int.bed) tmp.pe.zcat \
+  > tmp.pe.nodel.txt || true
+
+awk '{
+  if ($4>0)      print $1"@"$2, $1,$2, $4, $4+2, $5;
+  else           print $1"@"$2, $1,$2, $4, 2,    $5
+}' OFS="\t" tmp.pe.nodel.txt \
+| awk '!seen[$1"@"$2]++' \
+> pe_indiv_geno.nodel.txt
+
+cat pe_indiv_geno.del.txt pe_indiv_geno.nodel.txt > pe_indiv_geno.txt
+sort -k1,1 pe_indiv_geno.txt | gzip > pe_indiv_geno.txt.gz
+
+rm -f tmp.pe.zcat tmp.pe.del.txt tmp.pe.nodel.txt pe_indiv_geno.del.txt pe_indiv_geno.nodel.txt pe_indiv_geno.txt
 
-rm pe_indiv_geno.txt
 
 ##SR##
-zcat $srgeno_indiv_file \
-  | { fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) || true; } \
-  |awk '{if ($4>1) print $1"@"$2,$1,$2,$4,0,$5;else if ($4==1) print $1"@"$2,$1,$2,$4,1,$5 ;else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-  |awk '!seen[$1"@"$2]++' \
-  >sr_indiv_geno.txt
+zcat "$srgeno_indiv_file" > tmp.sr.zcat
+
+##Deletion events, need to PE-SR genotypes to match RD format (2==ref)##
+fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) tmp.sr.zcat \
+  > tmp.sr.del.txt || true
+
+awk '{
+  if ($4>1)      print $1"@"$2,$1,$2,$4,0,$5;
+  else if ($4==1)print $1"@"$2,$1,$2,$4,1,$5;
+  else           print $1"@"$2,$1,$2,$4,2,$5
+}' OFS="\t" tmp.sr.del.txt \
+| awk '!seen[$1"@"$2]++' \
+> sr_indiv_geno.del.txt
     
 ##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
-count_nonDEL2=$(awk '{if ($5!="DEL") print $4}' int.bed | wc -l)
-if [ "$count_nonDEL2" -gt 0 ]; then
-  zcat "$srgeno_indiv_file" \
-    | { fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) || true; } \
-    | awk '{if ($4>0) print $1"@"$2,$1,$2,$4,$4+2,$5; else print $1"@"$2,$1,$2,$4,2,$5}' OFS='\t' \
-    | awk '!seen[$1"@"$2]++' \
-    >> sr_indiv_geno.txt
-fi
-  
-sort -k1,1 sr_indiv_geno.txt|gzip>sr_indiv_geno.txt.gz
+fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) tmp.sr.zcat \
+  > tmp.sr.nodel.txt || true
+
+awk '{
+  if ($4>0)      print $1"@"$2,$1,$2,$4,$4+2,$5;
+  else           print $1"@"$2,$1,$2,$4,2,$5
+}' OFS="\t" tmp.sr.nodel.txt \
+| awk '!seen[$1"@"$2]++' \
+> sr_indiv_geno.nodel.txt
+
+cat sr_indiv_geno.del.txt sr_indiv_geno.nodel.txt > sr_indiv_geno.txt
+sort -k1,1 sr_indiv_geno.txt | gzip > sr_indiv_geno.txt.gz
+
+rm -f tmp.sr.zcat tmp.sr.nodel.txt tmp.sr.del.txt sr_indiv_geno.del.txt sr_indiv_geno.nodel.txt sr_indiv_geno.txt
 
-rm sr_indiv_geno.txt
 
 ##check to make sure PE and SR are same size which they should be##
 
-# if [ $(zcat sr_indiv_geno.txt.gz|wc -l) !=  $(zcat pe_indiv_geno.txt.gz|wc -l)  ] 
-# then
-#  echo "ERROR: PE and SR genotype files have different sizes"
-#  exit
-# fi
+if [ $(zcat sr_indiv_geno.txt.gz|wc -l) !=  $(zcat pe_indiv_geno.txt.gz|wc -l)  ] 
+then
+ echo "ERROR: PE and SR genotype files have different sizes"
+ exit
+fi
 
 ##All PE/SR .'s for samples missing RD##
 ##Add max PE/SR to use for future GQ integration##
@@ -92,7 +114,7 @@ join -j 1 -a 1 -e "." -o 1.1 1.2 1.3 1.4 1.5 2.4 2.5 2.6  \
   else if ($6>0 && $9==0) print $0 "\t" $6 "\t" $7 "\t" $8  ; \
   else if ($6==0 && $9>0) print $0 "\t" $9 "\t" $10 "\t" $11 ; \
   else if ($8>=$11)  print $0 "\t"$6 "\t" $7 "\t" $8  ; \
-  else if ($11>$8) print $0 "\t" $9 "\t" $10 "\t" $11 }' || true \
+  else if ($11>$8) print $0 "\t" $9 "\t" $10 "\t" $11 }' \
   |gzip \
   >RDall.combined.files.txt.gz
 
@@ -110,7 +132,7 @@ join -j 1 -a 2 -e "." -o 2.1 2.2 2.3 1.4 1.5 2.4 2.6  <(zcat rd_indiv_geno.txt.g
    |tr ' ' '\t' \
    |join -j 1 -o 1.1 1.2 1.3 1.4 1.5 1.6 1.7 2.4 2.6 - <(zcat sr_indiv_geno.txt.gz|sort -k1,1) \
    |tr ' ' '\t' \
-   |gzip || true \
+   |gzip \
    >PESRall.combined.files.txt.gz
 
 ##variant combine##
@@ -213,7 +235,7 @@ then
   | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
-   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' || true \
+   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($4==2 && $4==$7 && $4!=$10) print $0 "\t" "RD,PE" ; \
   else if ($4==2 && $4!=$7 && $4==$10) print $0 "\t" "RD,SR" ; \
@@ -221,11 +243,11 @@ then
   else if ($4!=2 && $7!=2 && $10!=2) print $0 "\t" "RD,PE,SR" ; \
   else if ($4!=2 && $7!=2 && $10==2) print $0 "\t" "RD,PE" ; \
   else if ($4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
-  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' || true \
+  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' \
   |cut -f1-6,8-9,11,15- \
   |awk '{if ($4>=2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,0,$11,$12; \
    else if ($4==1) print $1,$2,$3,$4,$5,$6,$7,$8,$9,1,$11,$12; \
-   else if ($4==0) print $1,$2,$3,$4,$5,$6,$7,$8,$9,2,$11,$12; }' || true \
+   else if ($4==0) print $1,$2,$3,$4,$5,$6,$7,$8,$9,2,$11,$12; }' \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
 
@@ -233,7 +255,7 @@ then
   | { fgrep -wf gt5kbcnv.del.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
-   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' || true \
+   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi
@@ -246,7 +268,7 @@ then
   | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($5==999) print $0,$4,999; \
    else if ($4==$13) print $0,$4,$5+((999-$5) * ($14/999)*0.5); \
-   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' || true \
+   else print $0,$4,$5-(($5-1) * ($14/999)*0.5) }' OFS='\t' \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($4==2 && $4==$7 && $4!=$10) print $0 "\t" "RD,PE" ; \
   else if ($4==2 && $4!=$7 && $4==$10) print $0 "\t" "RD,SR" ; \
@@ -254,10 +276,10 @@ then
   else if ($4!=2 && $7!=2 && $10!=2) print $0 "\t" "RD,PE,SR" ; \
   else if ($4!=2 && $7!=2 && $10==2) print $0 "\t" "RD,PE" ; \
   else if ($4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
-  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' || true \
+  else if ($4!=2 && $7==2 && $10==2) print $0 "\t" "RD" }' \
   |cut -f1-6,8-9,11,15- \
   |awk '{if ($4<=2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,0,$11,$12; \
-   else if ($4>2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10-2,$11,$12}' || true \
+   else if ($4>2) print $1,$2,$3,$4,$5,$6,$7,$8,$9,$10-2,$11,$12}' \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
 
@@ -265,7 +287,7 @@ then
   | { fgrep -wf gt5kbcnv.dup.ids.txt || true; } \
   |awk  '{if ($2==999) print $0,999; \
    else if ($3>=$4) print $0,$2+((999-$2) * ($3/999)*0.5); \
-   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' || true \
+   else if ($4>$3) print $0,$2+((999-$2) * ($4/999)*0.5);  }' \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi
@@ -284,7 +306,7 @@ then
   | { fgrep -wf gt1_5kbcnv.ids.txt || true; } \
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($4==$13) print $0,$12,$14+((999-$14) * ($5/999)*0.5); \
-  else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' || true \
+  else print $0,$12,$14-(($14-1) * ($5/999)*0.5) }' OFS='\t' \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($13==2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "RD,PE" ; \
   else if ($13==2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "RD,SR" ; \
@@ -296,7 +318,7 @@ then
   else if ($13!=2 && $4!=2 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
   else if ($13!=2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "SR" ; \
   else if ($13!=2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "PE"; \
-  else if ($13!=2 && $4==2 && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' || true \
+  else if ($13!=2 && $4==2 && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' \
   |cut -f1-6,8-9,11,15- \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
@@ -313,7 +335,7 @@ fi
 ###CNV <1kb and removing any CNV with no depth genotype####
 { fgrep -wvf <(zcat RDall.combined.files.txt.gz \
      |awk -F'\t' '{if ($4==".") print $2}') int.bed || true; } \
-  |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' || true \
+  |awk -F'\t' '{if (($5=="DUP" || $5=="DEL") && $3-$2<1000 ) print $4}' \
   >lt1kbcnv.ids.txt
 
 if [ $(cat lt1kbcnv.ids.txt|wc -l) -gt 0 ] 
@@ -324,7 +346,7 @@ then
   |awk  '{if ($14==999) print $0,$12,999; \
   else if ($7==$10 && $8>=$11) print $0,$12,$14+((999-$14) * ($11/999)*0.5); \
   else if ($7==$10 && $11>=$8) print $0,$12,$14+((999-$14) * ($8/999)*0.5); \
-  else  print $0 "\t" $12 "\t" $14}' OFS='\t' || true \
+  else  print $0 "\t" $12 "\t" $14}' OFS='\t' \
   |awk '{if ($4==$7 && $4==$10) print $0 "\t" "RD,PE,SR"; \
   else if ($13==2 && $4==2 && $7==2 && $10!=2) print $0 "\t" "RD,PE" ; \
   else if ($13==2 && $4==2 && $7!=2 && $10==2) print $0 "\t" "RD,SR" ; \
@@ -336,7 +358,7 @@ then
   else if ($13!=2 && $4==$13 && $7==2 && $10!=2) print $0 "\t" "RD,SR" ; \
   else if ($13!=2  && $7==2 && $10!=2) print $0 "\t" "SR" ; \
   else if ($13!=2  && $7!=2 && $10==2) print $0 "\t" "PE"; \
-  else if ($13!=2  && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' || true \
+  else if ($13!=2  && $7!=2 && $10!=2) print $0 "\t" "PE,SR" }' \
   |cut -f1-6,8-9,11,15- \
   |tr ' ' '\t' \
   >>genotype.indiv.txt
@@ -345,7 +367,7 @@ then
   | { fgrep -wf lt1kbcnv.ids.txt || true; } \
   |awk  '{if ($3==999 || $4==999) print $0,999; \
    else if ($3>=$4) print $0,$3+((999-$3) * ($2/999)*0.5); \
-   else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' || true \
+   else if ($4>$3) print $0,$4+((999-$4) * ($2/999)*0.5);  }' \
    |tr ' ' '\t' \
   >>genotype.variant.txt
 fi
@@ -382,4 +404,4 @@ cat genotype.indiv.txt \
 cat genotype.variant.txt \
   |awk '{if ($2==0) $2=1;if ($3==0) $3=1; if ($4==0) $4=1; if ($5==0) $5=1; print}' OFS="\t" \
   |gzip \
-  >genotype.variant.txt.gz
+  >genotype.variant.txt.gz
\ No newline at end of file

From ed2a5b1ca5af4cd2ea19b0f0f770960fe9c40781 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Thu, 23 Jan 2025 10:50:50 -0500
Subject: [PATCH 13/17] Added extra line

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index e76772f73..e01f260c8 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -404,4 +404,5 @@ cat genotype.indiv.txt \
 cat genotype.variant.txt \
   |awk '{if ($2==0) $2=1;if ($3==0) $3=1; if ($4==0) $4=1; if ($5==0) $5=1; print}' OFS="\t" \
   |gzip \
-  >genotype.variant.txt.gz
\ No newline at end of file
+  >genotype.variant.txt.gz
+  
\ No newline at end of file

From 82239a0061d1281c336b2a1ec01090c36b3b595b Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Fri, 24 Jan 2025 11:18:55 -0500
Subject: [PATCH 14/17] Modified to use ARGIND

---
 .../scripts/IntegrateGQ.sh                    | 107 ++++++++----------
 1 file changed, 48 insertions(+), 59 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index e01f260c8..4b618a38b 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -31,67 +31,56 @@ zcat $RD_melted_genotypes \
   >rd_indiv_geno.txt.gz
 
 ##PE##
-zcat "$pegeno_indiv_file" > tmp.pe.zcat
-
-##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
-fgrep -wf <(awk '{if ($5 == "DEL") print $4}' int.bed) tmp.pe.zcat \
-  > tmp.pe.del.txt || true
-  
-awk '{
-  if ($4>1)      print $1"@"$2, $1,$2, $4, 0, $5;
-  else if ($4==1)print $1"@"$2, $1,$2, $4, 1, $5;
-  else           print $1"@"$2, $1,$2, $4, 2, $5
-}' OFS="\t" tmp.pe.del.txt \
-| awk '!seen[$1"@"$2]++' \
-> pe_indiv_geno.del.txt
-
-##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
-fgrep -wf <(awk '{if ($5 != "DEL") print $4}' int.bed) tmp.pe.zcat \
-  > tmp.pe.nodel.txt || true
-
-awk '{
-  if ($4>0)      print $1"@"$2, $1,$2, $4, $4+2, $5;
-  else           print $1"@"$2, $1,$2, $4, 2,    $5
-}' OFS="\t" tmp.pe.nodel.txt \
-| awk '!seen[$1"@"$2]++' \
-> pe_indiv_geno.nodel.txt
-
-cat pe_indiv_geno.del.txt pe_indiv_geno.nodel.txt > pe_indiv_geno.txt
-sort -k1,1 pe_indiv_geno.txt | gzip > pe_indiv_geno.txt.gz
-
-rm -f tmp.pe.zcat tmp.pe.del.txt tmp.pe.nodel.txt pe_indiv_geno.del.txt pe_indiv_geno.nodel.txt pe_indiv_geno.txt
-
+zcat "$pegeno_indiv_file" | \
+awk -v OFS="\t" '
+  ARGIND==1 {
+    if ($5 == "DEL") {
+      del[$4]    # e.g. del["variant_id"]
+    } else {
+      nodel[$4]
+    }
+    next
+  }
+
+  ARGIND==2 {
+    if ($1 in del) {
+      final_gt = ($4>1 ? 0 : ($4==1 ? 1 : 2))
+      print $1"@"$2, $1, $2, $4, final_gt, $5
+    } else if ($1 in nodel) {
+      final_gt = ($4>0 ? $4+2 : 2)
+      print $1"@"$2, $1, $2, $4, final_gt, $5
+    }
+    # If $1 not in either array, do nothing.
+  }
+' int.bed - \
+| awk '!seen[$1]++' \
+| sort -k1,1 \
+| gzip > pe_indiv_geno.txt.gz
 
 ##SR##
-zcat "$srgeno_indiv_file" > tmp.sr.zcat
-
-##Deletion events, need to PE-SR genotypes to match RD format (2==ref)##
-fgrep -wf <(awk '{if ($5=="DEL") print $4}' int.bed) tmp.sr.zcat \
-  > tmp.sr.del.txt || true
-
-awk '{
-  if ($4>1)      print $1"@"$2,$1,$2,$4,0,$5;
-  else if ($4==1)print $1"@"$2,$1,$2,$4,1,$5;
-  else           print $1"@"$2,$1,$2,$4,2,$5
-}' OFS="\t" tmp.sr.del.txt \
-| awk '!seen[$1"@"$2]++' \
-> sr_indiv_geno.del.txt
-    
-##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
-fgrep -wf <(awk '{if ($5!="DEL") print $4}' int.bed) tmp.sr.zcat \
-  > tmp.sr.nodel.txt || true
-
-awk '{
-  if ($4>0)      print $1"@"$2,$1,$2,$4,$4+2,$5;
-  else           print $1"@"$2,$1,$2,$4,2,$5
-}' OFS="\t" tmp.sr.nodel.txt \
-| awk '!seen[$1"@"$2]++' \
-> sr_indiv_geno.nodel.txt
-
-cat sr_indiv_geno.del.txt sr_indiv_geno.nodel.txt > sr_indiv_geno.txt
-sort -k1,1 sr_indiv_geno.txt | gzip > sr_indiv_geno.txt.gz
-
-rm -f tmp.sr.zcat tmp.sr.nodel.txt tmp.sr.del.txt sr_indiv_geno.del.txt sr_indiv_geno.nodel.txt sr_indiv_geno.txt
+zcat "$srgeno_indiv_file" | \
+awk -v OFS="\t" '
+  ARGIND==1 {
+    if ($5 == "DEL") {
+      del[$4]
+    } else {
+      nodel[$4]
+    }
+    next
+  }
+  ARGIND==2 {
+    if ($1 in del) {
+      final_gt = ($4>1 ? 0 : ($4==1 ? 1 : 2))
+      print $1"@"$2, $1, $2, $4, final_gt, $5
+    } else if ($1 in nodel) {
+      final_gt = ($4>0 ? $4+2 : 2)
+      print $1"@"$2, $1, $2, $4, final_gt, $5
+    }
+  }
+' int.bed - \
+| awk '!seen[$1]++' \
+| sort -k1,1 \
+| gzip > sr_indiv_geno.txt.gz
 
 
 ##check to make sure PE and SR are same size which they should be##

From 73497801bf670eeb25cd83ecd83ef3335b1cb190 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Fri, 24 Jan 2025 18:50:58 -0500
Subject: [PATCH 15/17] Removed extra line in pe test

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 4b618a38b..f54493b4b 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -41,7 +41,6 @@ awk -v OFS="\t" '
     }
     next
   }
-
   ARGIND==2 {
     if ($1 in del) {
       final_gt = ($4>1 ? 0 : ($4==1 ? 1 : 2))

From 6512861a92d0ac009fff4f0f4b7f958ae231b733 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Fri, 24 Jan 2025 18:51:26 -0500
Subject: [PATCH 16/17] Removed extra space at the end of script

---
 src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index f54493b4b..2e5f66df5 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -393,4 +393,3 @@ cat genotype.variant.txt \
   |awk '{if ($2==0) $2=1;if ($3==0) $3=1; if ($4==0) $4=1; if ($5==0) $5=1; print}' OFS="\t" \
   |gzip \
   >genotype.variant.txt.gz
-  
\ No newline at end of file

From bd4473fe6d1024b521c14154d4aba9c64ddee6f3 Mon Sep 17 00:00:00 2001
From: Karan Jaisingh <kjaising@broadinstitute.org>
Date: Tue, 28 Jan 2025 15:16:33 -0500
Subject: [PATCH 17/17] Readded comments for user clarity

---
 .../04_variant_resolution/scripts/IntegrateGQ.sh           | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
index 2e5f66df5..3bdea0fb3 100755
--- a/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
+++ b/src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh
@@ -35,7 +35,7 @@ zcat "$pegeno_indiv_file" | \
 awk -v OFS="\t" '
   ARGIND==1 {
     if ($5 == "DEL") {
-      del[$4]    # e.g. del["variant_id"]
+      del[$4]
     } else {
       nodel[$4]
     }
@@ -43,13 +43,14 @@ awk -v OFS="\t" '
   }
   ARGIND==2 {
     if ($1 in del) {
+      ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
       final_gt = ($4>1 ? 0 : ($4==1 ? 1 : 2))
       print $1"@"$2, $1, $2, $4, final_gt, $5
     } else if ($1 in nodel) {
+      ##Duplications and other events, need to PE-SR genotypes to match RD (2==ref)##
       final_gt = ($4>0 ? $4+2 : 2)
       print $1"@"$2, $1, $2, $4, final_gt, $5
     }
-    # If $1 not in either array, do nothing.
   }
 ' int.bed - \
 | awk '!seen[$1]++' \
@@ -69,9 +70,11 @@ awk -v OFS="\t" '
   }
   ARGIND==2 {
     if ($1 in del) {
+      ##Deletions, need to PE-SR genotypes to match RD format (2==ref)##
       final_gt = ($4>1 ? 0 : ($4==1 ? 1 : 2))
       print $1"@"$2, $1, $2, $4, final_gt, $5
     } else if ($1 in nodel) {
+      ##Duplications and other events, need to PE-SR genotysrs to match RD (2==ref)##
       final_gt = ($4>0 ? $4+2 : 2)
       print $1"@"$2, $1, $2, $4, final_gt, $5
     }