Question: Snp Calling + Somatic Mutation On X & Y Chromosomes
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gravatar for ananth.ccamp
6.6 years ago by
ananth.ccamp0 wrote:

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

somatic chromosome • 2.3k views
ADD COMMENTlink modified 6.6 years ago by Chris Miller21k • written 6.6 years ago by ananth.ccamp0
2
gravatar for Matt Miossec
6.6 years ago by
Matt Miossec330
Universidad Andrés Bello
Matt Miossec330 wrote:

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

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Matt Miossec330
0
gravatar for Buttonwood
6.6 years ago by
Buttonwood40
China
Buttonwood40 wrote:

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

ADD COMMENTlink written 6.6 years ago by Buttonwood40
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