Exome data: how to filter by cases and controls?

[Sini]

Hi all,

I'm currently trying to figure out how to sort the exome data from several samples so that I would have a list with SNPs/indels including the SNPs/Indels shared by all of the patients and none of the controls.

i.e. I would like to filter out all of the SNPs/indels from the controls and find a common mutation in the cases.

Does anyone know some nice program that could do this? I tried to use exome-assistant, but it seems to accept only data in hg18 format... My data is hg19.

Sincerely,
Sini

[ersgupta]

I think BEDtools should be able to do this...
For instance, you can merge the SNPs/INDELs(using mergeBed), use multiInteresectBed for getting SNPs/INDELs common to all cases, then use subtractBed to get case specific variants.

[Sini]

Thank you ersgupta! I'll look into BEDtools