Remove Known Snps From A Vcf File

Question

[Philipp]

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

Answer 1

[Pierre Lindenbaum]

• 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.

[User 59]

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