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6 votes

A bash script for running on a bunch of bam files

There are a couple ways to approach this, one is to create output files based on the BAM input file name - the other approach is to make a new folder (based on the ...
Scot's user avatar
  • 782
5 votes

Singularity & GATK CreateSequenceDictionary

This has nothing to do with Singularity/Docker or GATK. You get the error .dict: command not found because you've used backticks to perform a command substitution ...
Steve's user avatar
  • 3,079
4 votes

How to adjust cutoffs in Mutect2

Mutect2 uses a statistical model based on the available reads. Unlike with some other tools, there is not threshold based on depth or VAF or QUAL. The main statistic that does govern emission is the ...
Yossi Farjoun's user avatar
3 votes

How to run a GATK Docker Image with local files?

Read the manual please: -v or --volume: Consists of three fields, separated by ...
Ram RS's user avatar
  • 2,279
2 votes

Getting VCF file that contain common SNPs from 6 VCF file using isec

You've used the right tool and gotten the right results. What you need to understand is that VCF contains variant loci as well as the genotypes for >=1 sample(s) at those loci. The intersect ...
Ram RS's user avatar
  • 2,279
2 votes

I am trying to create a subset of 10k variants from 25-30 unmapped contigs of a g.vcf file including the header

After some guidance from my advisor, this command allowed me to get the output file I needed. ...
Lauren Sabo's user avatar
1 vote

Importing local files to a GATK docker image

@terdon answered that docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest
Zizogolu's user avatar
  • 2,132
1 vote

WES variant calling with DNBSEQ-T7: technical quality assessment

Okay it seems the company has given you the VCF (maybe), you want to re-run it via Mutect2. Mutect2 is part of the GATK suite, it's an upgrade, and they are refusing to run the appropriate PON. I ...
M__'s user avatar
  • 12.1k
1 vote

GATK SplitIntervals: A USER ERROR has occurred: but no positional argument is defined for this tool

This solution where the -O is just set to the output directory seems the most easy way to handle the issue: Keep the following variables the same: ...
Indira's user avatar
  • 380
1 vote

GATK g CNV code Aborts Before Running Main Code

You are using ${CHROMOSOME_NAMES[@]} but you never define that, so when your code gets here: ...
terdon's user avatar
  • 9,846

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