Snp Calling + Somatic Mutation On X & Y Chromosomes

Question

[ananth.ccamp]

Dear All,

I have got few somatic mutation hits on X & Y chromosomes using both varscan and somatic sniper tools. Are these false positives hits? Somatic mutations occur only on non-sex chromosomes I believe. Should I run these tools only for non-sex chromosomes?

Any information highly appreciated.

Ananth

Answer 1

[Matthieu Miossec]

You're mixing up sex chromosomes with germ-line (sex) cells. So no, they're not necessarily false positives.

Answer 2

[Buttonwood]

You can check if the snp scorce or coverage is very low, so these snps may be sequence errors.