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!
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ThunderPhoenix •
tabix --print-header in.vcf.gz "chr1:234-567"
should output a valid VCF.
but bcftools remains the tool of choice.
vcftools is deprecated.
Would the Site Filtering Options in the vcftools manual work?
Actually I just used bcftools view and subset the specified chromosome. I'd imagine subsetting via vcftools would be equivalently good.
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