Question: Comparison of SNPs between groups of samples
1
gravatar for agata88
13 months ago by
agata88770
Poland
agata88770 wrote:

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 • 679 views
ADD COMMENTlink modified 13 months ago by Pierre Lindenbaum119k • written 13 months ago by agata88770
1
gravatar for Pierre Lindenbaum
13 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

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

ADD COMMENTlink written 13 months ago by Pierre Lindenbaum119k

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?

ADD REPLYlink written 13 months ago by agata88770

what would be the

"kind of SNP patterns,"

here ?

ADD REPLYlink written 13 months ago by Pierre Lindenbaum119k

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.

ADD REPLYlink written 13 months ago by agata88770

and you'll need a statistical test ...

ADD REPLYlink written 13 months ago by Pierre Lindenbaum119k

to show significant difference at p< 0,05.

ADD REPLYlink written 13 months ago by agata88770
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