Snp Calling + Somatic Mutation On X & Y Chromosomes
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
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Chris Miller
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ananth.ccamp •
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ananth.ccamp •
2 answers
You're mixing up sex chromosomes with germ-line (sex) cells. So no, they're not necessarily false positives.
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Matthieu Miossec
You can check if the snp scorce or coverage is very low, so these snps may be sequence errors.
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Buttonwood •
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