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Flag possible cross-sample contamination of normal DNA in tumor samples #138

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mfoll opened this issue Oct 20, 2016 · 0 comments

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mfoll commented Oct 20, 2016

This causes false positive somatic mutations and has been described here for example (Mutect is using this information too):
http://bioinformatics.oxfordjournals.org/content/27/18/2601.long
http://bioinformatics.oxfordjournals.org/content/32/20/3196.long
In our case as we are calling all samples together we can simply flag mutations that would be classified as somatic by #133 but that are also found as germline in another sample.

mfoll added the enhancement label

mfoll assigned nalcala

nalcala added a commit that referenced this issue


          beta implementation of #137 and #138 (to check)

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mfoll mentioned this issue

Variant calling using tumor/normal pairs #144

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mfoll closed this as completed

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