How to create a new VCF file with subsetted data

Question

[ThunderPhoenix]

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!

Answer 1

[Pierre Lindenbaum]

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

should output a valid VCF.

but bcftools remains the tool of choice.

vcftools is deprecated.

Answer 2

[chefer]

Would the Site Filtering Options in the vcftools manual work?

[ThunderPhoenix]

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

[Ram]

Please accept their answer to mark the post as solved.