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

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.

variant-calling vcf snps
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updated by Ashutosh Pandey Ashutosh Pandey • written by robjohn7000 robjohn7000

1 answer

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

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written by Ashutosh Pandey Ashutosh Pandey

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

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written by robjohn7000 robjohn7000

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