Snp Calling + Somatic Mutation On X & Y Chromosomes
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11.3 years ago

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 • 3.3k views
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2
Entering edit mode
11.3 years ago

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

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11.3 years ago
Buttonwood ▴ 40

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

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