Question

cut mt,x and unknown chromosomes

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6.3 years ago

Siavash Salek Ardestani ▴ 20

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?

vcf SNP snp • 1.2k views

ADD COMMENT • link updated 6.3 years ago by Alex Reynolds 35k • written 6.3 years ago by Siavash Salek Ardestani ▴ 20

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

ADD REPLY • link 6.3 years ago by GouthamAtla 12k

score 0 · Answer 1 · 2018-01-14

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6.3 years ago

Alex Reynolds 35k

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

ADD COMMENT • link 6.3 years ago by Alex Reynolds 35k