Parsing Vcf Files For Snps/Indels And Comparing Extracted Varaints Among Bacteria Spp.

Question

[robjohn7000]

Hi,

I have many VCF files (each for different bacteria spp.) for SNPs/INDELs that I just want to extract SNPs/INDELs from. Then I will like to compare these variants in each file against each other to find which SNPs/INDELs are common/absent in each file. I'm new to this kind of analysis, and would be pleased if someone could advice me on any available tools or computational steps/scripts (R, Python, Perl) most appropriate for what I want to achieve.

Thanks in advance.

Answer 1

[Ashutosh Pandey]

Vcftools (http://vcftools.sourceforge.net) should be able to perform most of the things you need.

[robjohn7000]

Thanks so much Ashutosh. I have had a look and it's certainly what I want. Much appreciated!