Question: Filtering vcf FORMAT?
3
gravatar for amber.zqt
2.2 years ago by
amber.zqt30
amber.zqt30 wrote:

I have a vcf file with contains GT:DS:GP for FORMAT field, how can i only keep the GT? The vcftools "--extract-FORMAT-info GT" command will at the same time filtering all other columns. But i wish to keep those.

snp vcf • 1.2k views
ADD COMMENTlink modified 2.2 years ago by Pierre Lindenbaum127k • written 2.2 years ago by amber.zqt30
4
gravatar for Pierre Lindenbaum
2.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

https://samtools.github.io/bcftools/bcftools.html

... and "FORMAT" to remove all FORMAT tags except GT.

bcftools annotate -x 'FORMAT' in.vcf
ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Pierre Lindenbaum127k
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