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7.5 years ago
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?
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?
Use grep
; see my previous answer in the vcf2bed question.
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Make a bed file with chr coordinates (chromosome length). Intersect VCF with the chr bed file using bedtools.