VCF compare tools

Question

[mohanapriyagovindaraju]

I am new to VCF tool analysis,i have three VCFcombined datasets for indel and SNPs.Hereafter i need to compare all three datasets. When i compared an output shows empty.Any other tools for VCF compare further analyis of datasets.

Advance Thanks&Regards,

Answer 1

[Medhat]

First I think this should be a Question not a Tool.

If you means by compare intersect you can use bedtools

or you can use vcf-cmpare

Compares positions in two or more VCF files and outputs the numbers of positions contained in one but not the other files; two but not the other files, etc, which comes handy when generating Venn diagrams. The script also computes numbers such as nonreference discordance rates (including multiallelic sites), compares actual sequence (useful when comparing indels), etc.

also SnpSift is very hany tool