Question: Adding allele frequency to the genotype field of a VCF file
0
gravatar for Nonny27
4.6 years ago by
Nonny270
Nonny270 wrote:

I'm wondering if there is an way to get the allele frequency (AF1) from the INFO field VCF file into the genotype field instead (or as well), that way when I merge these files into a multi-sample VCF I can still easily access this information.

I have managed to isolate the allele frequency values from the INFO column using a sed command based on the flanking strings:

sed -e 's/.*;AF1=\(.*\);AN.*/\1/' file.vcf > output.txt

However, I can't work out how to append this to the genotype field. ie. GT:GQ:PL:AF1

Any help would be greatly appreciated!

sequencing snp next-gen • 1.9k views
ADD COMMENTlink modified 4.5 years ago by Zev.Kronenberg11k • written 4.6 years ago by Nonny270
0
gravatar for Zev.Kronenberg
4.5 years ago by
United States
Zev.Kronenberg11k wrote:

VCFFIXUP in vcflib should do what you want.

https://github.com/vcflib/vcflib

ADD COMMENTlink written 4.5 years ago by Zev.Kronenberg11k
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