how to extract the variants using Bed file
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6.3 years ago

Hello all,

Sorry if this has been answered before (though I have not found an appropriate answer already) What is an effective way to extract multiple variants from the vcf file using bed file.

I have a huge number of variants in vcf. example i have downloaded the human whole genome vcf. but i am looking for certain exons variants and i have those position in the bed file. i want to find only check those positions alone not the whole vcf. how to extract the variants using Bed file 

next-gen sequencing bedfile variant_calling • 4.1k views
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Entering edit mode
6.3 years ago

The site filtering options in VCFtools has a --bed command, which allows the user to extract or filter variant using a bed file. 

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