Question

How to create a new VCF file with subsetted data

0

Entering edit mode

2.5 years ago

ThunderPhoenix • 0

Hello! So, lets say I have a sorted, indexed (tabix) VCF file, and wanted to make a new subsetted VCF file out of the that contains only a specific region from chr1. In that case, I know that tabix chr1.vcf.gz:<start>-<end> will give you the raw subsetted genotype data. How do I create a valid VCF file out of this? Thanks!

vcf tabix subset • 1.2k views

ADD COMMENT • link updated 2.3 years ago by Ram 44k • written 2.5 years ago by ThunderPhoenix • 0

1

Entering edit mode

2.5 years ago

chefer ▴ 350

Would the Site Filtering Options in the vcftools manual work?

ADD COMMENT • link 2.5 years ago by chefer ▴ 350

0

Entering edit mode

Actually I just used bcftools view and subset the specified chromosome. I'd imagine subsetting via vcftools would be equivalently good.

ADD REPLY • link 2.5 years ago by ThunderPhoenix • 0

0

Entering edit mode

Please accept their answer to mark the post as solved.

ADD REPLY • link 2.5 years ago by Ram 44k

score 4 · Accepted Answer · 2022-06-30

4

Entering edit mode

2.5 years ago

Pierre Lindenbaum 164k

tabix --print-header in.vcf.gz "chr1:234-567"

should output a valid VCF.

but bcftools remains the tool of choice.

vcftools is deprecated.

ADD COMMENT • link 2.5 years ago by Pierre Lindenbaum 164k