Vcftools order of operations for filtering?

Question

[aj]

Can anyone point me where to find the order of operations used by vcftools when filtering? I need to apply many filters to some large vcfs to create smaller ones, and I need to make sure that individual filters are applied before MAF filters. But I cannot seem to find any documentation of the order that filters are applied.

Answer 1

[Pierre Lindenbaum]

vcftools is deprecated, use bcftools.

if you have any doubt about the order of the filters , pipe a filter into another one

bcftools view -i 'INFO/x1<1' -O u input.vcf | bcftools view --apply-filters 'PASS,.' -O u | bcftools view -O v -o out.vcf