Remove Known Snps From A Vcf File

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

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updated 14.4 years ago by Pierre Lindenbaum

• written 14.4 years ago by Philipp •

1 answer

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.

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updated 6.9 years ago by Ram

• written 14.4 years ago by Pierre Lindenbaum

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

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updated 6.9 years ago by Ram

• written 14.4 years ago by User 59

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