Question

Remove Known Snps From A Vcf File

1

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12.8 years ago

Philipp ▴ 20

Hi, I have a .vcf file with SNPs informations and I will remove all known SNPs which are reported in a database (e.g. dbSNP). Is there any software for this problem?

Thanks

vcf dbsnp • 6.7k views

ADD COMMENT • link updated 12.8 years ago by Pierre Lindenbaum 164k • written 12.8 years ago by Philipp ▴ 20

Ram · Answer 1 · 2012-03-12

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12.8 years ago

Pierre Lindenbaum 164k

download dbSNP as VCF ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/v4.0/
use bedtools ( http://code.google.com/p/bedtools/wiki/Usage#intersectBed) to remove those SNPs from your VCF.

ADD COMMENT • link updated 5.3 years ago by Ram 44k • written 12.8 years ago by Pierre Lindenbaum 164k

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Or you could use vcftools http://vcftools.sourceforge.net/perl_module.html#vcf-isec

ADD REPLY • link updated 5.3 years ago by Ram 44k • written 12.8 years ago by User 59 13k