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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 ...
Scot's user avatar
  • 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 ...
terdon's user avatar
  • 10.2k
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 ...
user438383's user avatar
  • 1,689
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 ...
winni2k's user avatar
  • 2,286
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
Zizogolu's user avatar
  • 2,160
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
  • 12.6k
1 vote

Error in running Mutect2

Downloading that vcf file from this link fixes the problem (but generates a new one) ...
Zizogolu's user avatar
  • 2,160

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