Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
bwa GATK4 read group issues wbsimey Bioinformatics 2 01-22-2020 08:38 AM
Mutect2 tumor-only - missing CHROM, ID, QUAL and FILTER columns in output vcf alzbeta_h Bioinformatics 0 03-05-2019 04:14 PM
GATK4, bash script... step CreateSequenceGroupingTSV echo manolis Bioinformatics 1 01-24-2018 01:06 PM
mutect2 in a targeted region lre1234 Bioinformatics 0 03-04-2016 09:16 AM

Thread Tools
Old 10-11-2019, 05:58 AM   #1
Junior Member
Location: Florence

Join Date: May 2019
Posts: 1
Unhappy GATK4 ( Mutect2 --germline-resource option

Hi everybody,

I am new analyzing WES and I try GATK4 workflow for the detection of somatic variants.

I run Mutect2 in tumor-only mode with these commands:

gatk Mutect2 -R reference.ucsc.hg19.fasta -L Target.bed -I input.bam --f1r2-tar-gz input.tar.gz -O output1.unfiltered.vcf --germline-resource af-only-gnomad.raw.sites.hg19.vcf [max-population-af default value = 0.01]

gatk Mutect2 -R reference.ucsc.hg19.fasta -L Target.bed -I input.bam --f1r2-tar-gz input.tar.gz -O output2.unfiltered.vcf [max-population-af default value = 0.01]

For the first command I obtained a vcf with around 40000 variants whereas with the second a vcf with around 100000 variants. I expected that --germline-resource filters out germline variants based on AF in the resource (af-only-gnomad.raw.sites.hg19.vcf).
However I notice that output1.unfiltered.vcf contains variants with POPAF (negative log 10 population allele frequencies of alt alleles) values that correspond to AF (in the resource) more than 0.01.

Does anybody know the logic used by Mutect2 to filter out variants based on germline resource? Is possible that Mutect2 consider other parameters than AF in the resource?

Thank you,
Simoner is offline   Reply With Quote

allele frequency, filter, gatk, germline-resource, mutect2

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 02:30 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO