cut mt,x and unknown chromosomes

Question

[Siavash Salek Ardestani]

I have many 'Un' (I think this is unknown chromosomes SNP) in a vcf file. how can I split or cut mt,x and unknown chromosomes from vcf?

[GouthamAtla]

Make a bed file with chr coordinates (chromosome length). Intersect VCF with the chr bed file using bedtools.

Answer 1

[Alex Reynolds]

Use grep; see my previous answer in the vcf2bed question.