Question: Parsing Vcf Files For Snps/Indels And Comparing Extracted Varaints Among Bacteria Spp.
gravatar for robjohn7000
6.3 years ago by
United Kingdom
robjohn700090 wrote:


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 • 3.4k views
ADD COMMENTlink modified 6.3 years ago by Ashutosh Pandey12k • written 6.3 years ago by robjohn700090
gravatar for Ashutosh Pandey
6.3 years ago by
Ashutosh Pandey12k wrote:

Vcftools ( should be able to perform most of the things you need.

ADD COMMENTlink written 6.3 years ago by Ashutosh Pandey12k

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

ADD REPLYlink written 6.3 years ago by robjohn700090
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