Filter mutect2 variants

genepi · Mar 7, 2024 · e6e2ae5 · e6e2ae5
1 parent 7a2d21c
commit e6e2ae5
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Showing 2 changed files with 16 additions and 11 deletions.
diff --git a/modules/local/mutect2.nf b/modules/local/mutect2.nf
@@ -36,18 +36,23 @@ process MUTECT2 {
         -R ${reference} \
         --min-reads-per-strand 2 \
         -V raw.vcf.gz \
-        --tmp-dir \$PWD \
+        --tmp-dir . \
         -O ${bam_file.baseName}.vcf.gz
 
     bcftools norm \
         -m-any \
         -f ${reference} \
         -o ${bam_file.baseName}.norm.vcf.gz -Oz \
         ${bam_file.baseName}.vcf.gz 
+
+    bcftools view \
+    -i 'FORMAT/AF>=${params.detection_limit}' \
+    -o ${bam_file.baseName}.vcf.gz -Oz \
+    ${bam_file.baseName}.norm.vcf.gz 
     
-    mv ${bam_file.baseName}.norm.vcf.gz ${bam_file.baseName}.vcf.gz
     tabix -f ${bam_file.baseName}.vcf.gz
 
+    rm ${bam_file.baseName}.norm.vcf.gz 
     rm raw.vcf.gz
     """
 }
diff --git a/tests/mitocalling.nf.test.snap b/tests/mitocalling.nf.test.snap
@@ -1,17 +1,17 @@
 {
     "Runs with single BAM file and mutect2": {
         "content": [
-            "variants.annotated.txt:md5,2df787e5b0067dc97f410c2aaf280285"
+            "variants.annotated.txt:md5,68e69c74076a094f90fcd148d24c107a"
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.04.2"
         },
-        "timestamp": "2024-03-03T13:36:56.200643224"
+        "timestamp": "2024-03-07T22:54:43.41727058"
     },
     "Runs with 6 samples provided as testdata with mutect2": {
         "content": [
-            "variants.annotated.txt:md5,60f38bd59aaa986644d1df365ae62948",
+            "variants.annotated.txt:md5,41d22ff665a2621d1eca7b9e07741368",
             {
                 "tasksFailed": 0,
                 "tasksCount": 28,
@@ -20,9 +20,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "22.10.4"
+            "nextflow": "23.04.2"
         },
-        "timestamp": "2024-03-04T13:37:55.902842"
+        "timestamp": "2024-03-07T23:01:31.253552492"
     },
     "Runs with single BAM file and mutserve": {
         "content": [
@@ -32,7 +32,7 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.2"
         },
-        "timestamp": "2024-03-03T13:53:38.360857477"
+        "timestamp": "2024-03-07T22:53:04.753352089"
     },
     "Runs with BAM file including different header contigs": {
         "content": [
@@ -70,9 +70,9 @@
         ],
         "meta": {
             "nf-test": "0.8.4",
-            "nextflow": "22.10.4"
+            "nextflow": "23.04.2"
         },
-        "timestamp": "2024-03-04T13:39:42.589344"
+        "timestamp": "2024-03-07T23:06:50.681516749"
     },
     "Runs with 6 samples provided as testdata with mutserve": {
         "content": [
@@ -87,6 +87,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.04.2"
         },
-        "timestamp": "2024-03-03T14:00:27.656567299"
+        "timestamp": "2024-03-07T22:57:49.179958661"
     }
 }