cut mt,x and unknown chromosomes
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?
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Alex Reynolds
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Siavash Salek Ardestani •
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written
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Siavash Salek Ardestani •
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Use grep; see my previous answer in the vcf2bed question.
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Alex Reynolds
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Make a bed file with chr coordinates (chromosome length). Intersect VCF with the chr bed file using bedtools.