更新 'tasks/gatk.wdl'

tasks/gatk.wdl

@@ -23,6 +23,7 @@ task gatk {
         bed="./gatk4_database/S07604514_Padded_use.bed"
         pon="./gatk4_database/somatic-hg38_1000g_pon.hg38.vcf.gz"
         EXAC="./gatk4_database/somatic-hg38_small_exac_common_3.hg38.vcf.gz"
+        GNOMAD="./gatk4_database/somatic-hg38_af-only-gnomad.hg38.vcf.gz"
         
         mkdir markduplicate
         mkdir BQSR
@@ -38,7 +39,7 @@ task gatk {
         gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" ApplyBQSR  -I ./markduplicate/${sample_id}_marked.bam  -R $hg38_genome -L $bed --bqsr-recal-file ./BQSR/${sample_id}_markdup_bqsr.report   -O ./BQSR/${sample_id}_markdup_bqsr.bam
         echo "BQSR done"
 
-        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" Mutect2 -R $hg38_genome -I ./BQSR/${sample_id}_markdup_bqsr.bam  -L $bed --pon $pon --germline-resource $dbsnp --tumor-lod-to-emit 2 --f1r2-tar-gz Mutect2/${sample_id}.f1r2.tar.gz  -O Mutect2/${sample_id}_mutect2_raw.vcf
+        gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" Mutect2 -R $hg38_genome -I ./BQSR/${sample_id}_markdup_bqsr.bam  -L $bed --pon $pon --germline-resource $GNOMAD --tumor-lod-to-emit 2 --f1r2-tar-gz Mutect2/${sample_id}.f1r2.tar.gz  -O Mutect2/${sample_id}_mutect2_raw.vcf
         echo "Mutect2 done"
 
         gatk --java-options "-Djava.io.tmpdir=./BQSR -Xms40G -Xmx40G -XX:ParallelGCThreads=2" GetPileupSummaries -R $hg38_genome -I ./BQSR/${sample_id}_markdup_bqsr.bam  -V $EXAC -L $EXAC -L $bed --interval-set-rule INTERSECTION  -O Mutect2/${sample_id}.getpileupsum.table