From 7dd55d1eb448a14a0c085944d5012d47241e59e4 Mon Sep 17 00:00:00 2001 From: Matteo Barcella Date: Fri, 4 Aug 2023 10:33:40 +0000 Subject: [PATCH] Update README.md --- WES/README.md | 5 ----- 1 file changed, 5 deletions(-) diff --git a/WES/README.md b/WES/README.md index d4413ad..9700f65 100644 --- a/WES/README.md +++ b/WES/README.md @@ -35,11 +35,6 @@ Below the workflow and commands used: ``` - gatk Mutect2 -I SampleID.disambiguatedSpeciesA.bam.sorted.bam -O Mutect2_raw_call_SampleID_exome_refseq_light.vcf.gz -R GRCh38.p13.genome.fa -L exome_light.bed -G StandardMutectAnnotation -OVI true -OVM true -ip 50 - gatk FilterMutectCalls -R GRCh38.p13.genome.fa -V Mutect2_raw_call_SampleID_exome_refseq_light.vcf.gz -O Mutect2_raw_call_SampleID_exome_refseq_light_filtered.vcf.gz -- bcftools view -i 'FORMAT/DP>10' Mutect2_raw_call_SampleID_exome_refseq_light_filtered.vcf.gz -O z > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz -- bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[%DP\t]\t[%AD\t]\t[%AF\t]\t[%GT\t]\n' Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_fields.txt -- bcftools view -f PASS Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10.vcf.gz -O z > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS.vcf.gz -- bcftools query -f '%CHROM\t%POS\t%REF\t%ALT\t[%DP\t]\t[%AD\t]\t[%AF\t]\t[%GT\t]\n' Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS.vcf.gz > Mutect2_raw_call_SampleID_exome_refseq_light_filtered_DP10_PASS_fields.txt - ``` # Annotation # -- GitLab