Overview
vk filter (REF|HET|ALT|MISSING) [--min=<min> --max=<max> --soft-filter=<soft> --mode=<mode>] <vcf>
The filter command can be used to hard or soft-filter variants based on the count or frequency of homozygous reference, heterozygous, homozygous alternative, or missing variants from a VCF.
Options
- --min=
- Set a minimum threshold for the specified filter. An integer is interpretted as a minimum count. A float is interpretted as a minimum frequency. - --max=
- Set a maximum threshold for the specified filter. An integer is interpretted as a maximum count. A float is interpretted as a maximum frequency. - --soft-filter=
- When sepcified, the filter is added to the FILTER
column and variants are NOT removed. - --mode=(+|x) - Specifies the mode for soft-filtering. When set to
+
, the filter is added to existing filters in the FILTER column. When set tox
the soft-filter replaces existing filters in the FILTER column.
Examples
The command below will return only variants with at least one homozygous REF and one homozygous ALT call:
vk filter REF --min=1 <vcf> | vk filter ALT --min=1 - | bcftools view -O z > one_homozygous.vcf.gz
The command below will soft-filter variants with greater than 10% missing calls.
vk filter MISSING --max=0.90 --soft-filter=HIGH-MISSING --mode=x <vcf>
Return variants with a no more than 3 heterozygous calls:
vk filter HET --max=3 <vcf>