Merge pull request #41 from broadinstitute/lfleming1022-patch-1

Update CollectSamErrorMetrics.wdl
broadinstitute · Sep 8, 2023 · 0da4b3c · 0da4b3c
2 parents 2b623f4 + eb26554
commit 0da4b3c
Showing 1 changed file with 14 additions and 3 deletions.
diff --git a/CollectSamError/CollectSamErrorMetrics.wdl b/CollectSamError/CollectSamErrorMetrics.wdl
@@ -43,15 +43,26 @@ task CollectSamErrorMetricsTask {
         File intervals
         Int disk_gb = 400
         Int memory_gb = 16
+        Int minMQ = 60
+        Float probability = 1.0
+
     }
     command {
         java -Xms2000m -jar /usr/gitc/picard.jar CollectSamErrorMetrics I=~{input_bam} \
-        O=~{output_name} R=~{ref_fasta} V=~{vcf_file} L=~{intervals} \
+        O=~{output_name} R=~{ref_fasta} V=~{vcf_file} L=~{intervals} MQ=~{minMQ} P=~{probability} \
         ERROR_METRICS=null \
         ERROR_METRICS="ERROR:INSERT_LENGTH" \
         ERROR_METRICS="ERROR:CYCLE" \
         ERROR_METRICS="ERROR:GC_CONTENT" \
-        ERROR_METRICS="ERROR"
+        ERROR_METRICS="ERROR:BASE_QUALITY" \
+        ERROR_METRICS="ERROR:ONE_BASE_PADDED_CONTEXT" \
+        ERROR_METRICS="ERROR:HOMOPOLYMER" \
+        ERROR_METRICS="OVERLAPPING_ERROR:INSERT_LENGTH" \
+        ERROR_METRICS="OVERLAPPING_ERROR:CYCLE" \
+        ERROR_METRICS="OVERLAPPING_ERROR:GC_CONTENT" \
+        ERROR_METRICS="OVERLAPPING_ERROR:BASE_QUALITY" \
+        ERROR_METRICS="OVERLAPPING_ERROR:ONE_BASE_PADDED_CONTEXT" \
+        ERROR_METRICS="OVERLAPPING_ERROR:HOMOPOLYMER"
 
     }
     output {
@@ -63,4 +74,4 @@ task CollectSamErrorMetricsTask {
         memory: memory_gb + "GB"
         cpu: "1"
     }
-}
+}