Sort VCFs based on chromosome, position, ref and alt
The commonly used vcf-sort (https://github.com/vcftools/vcftools/blob/master/src/perl/vcf-sort) resorts to sorting on chromosome and position only (sort -k1,1V -k2,2n), and on matches, will sort on full line (GNU sort last resort). This will in practice mean that a consistent sort on variants (chrom, pos, ref, alt) is not possible, as this is only true if the ID column is matching.
Take the following examples:
#CHROM POS ID REF ALT QUAL FILTER INFO
1 123 . GG A . . .
1 123 . G A . . .
#CHROM POS ID REF ALT QUAL FILTER INFO
1 123 some_id GG A . . .
1 123 another_id G A . . .
These files have the same variants, but will be sorted different by vcf-sort due to the differing ID field.
This package re-implements vcf-sort -c with the addition of -k4,5 to sort consistently on full variants.
- bash
- GNU coreutils
NOT Perl