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Comparison of SNPs between groups of samples

Hi all!

Could you please recommend a tool that can statistically compare SNPs between two groups of vcf's?

To be more clear, I have 30 vcf files for healthy patients, and 30 for sick patients. I need to search for some kind of SNP patterns, statistically significant between those two groups.

Any idea how to perform such analysis?

Thanks in advance,

Agata

snp
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by agata88 agata88

1 answer

run a fisher test for those variants. https://en.wikipedia.org/wiki/Fisher%27s_exact_test

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, it's one way. I'am thinking about something different.

What is on my mind is to go back to variant detection step and use VarScan Somatic caller. I might use samtools mpileup to generate two vcf's each containing variants for 30 samples. Do you think it's good idea?

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written by agata88 agata88

what would be the

"kind of SNP patterns,"

here ?

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written by Pierre Lindenbaum Pierre Lindenbaum

I would like to see whether there are variants that occur only in sick patients and not in healthy group. In addition, I would like to see that in multiple samples comparison. For example, let's say I've found 5 mutations that occur in 20 sick samples and not occur in healthy group at all - this 5 mutation will create some kind of pattern.

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written by agata88 agata88

to show significant difference at p< 0,05.

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written by agata88 agata88

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