6
votes
Accepted
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 ...
- 782
5
votes
Accepted
What are values of FILTER column of vcf files produced by Mutect2
You haven't told us what commands you ran, so I am assuming you first ran Mutect2 and then FilterMutectCalls. If so, the ...
- 9,662
3
votes
Accepted
Extracting a column from a vcf file
Either the zcat command or gunzip -c will decompress the file in a streaming fashion to the standard output without writing the ...
- 1,679
2
votes
Error in running Mutect2
Your input file pon.vcf.gz should be a gzip file, but from your file command it looks like it is an HTML file instead. Perhaps ...
- 2,236
1
vote
Accepted
Importing local files to a GATK docker image
@terdon answered that
docker run -v /data/Continuum/WES/:/gatk/vcf -it broadinstitute/gatk:latest
- 1,981
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__♦
- 11.9k
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