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nygenome / Conpair

Concordance and contamination estimator for tumor–normal pairs
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how to find the Tumor of the swapped samples #2

Closed tangwei1129 closed 7 years ago

tangwei1129 commented 7 years ago

I have used the Conpair to find the swapped samples successfully, but I came with new issue is how can I be sure that which sample is the Tumor samples? Thank you

ewabergmann commented 7 years ago

Conpair shows concordance between two samples based on the set of germline markers. Based on this value you cannot tell which sample is tumor and which is normal.

There are 2 things you could potentially do, both are based on the assumption that the tumor sample would contain multiple LOH events (which won't be true for quiet tumors with few CNVs): 1) based on the pileup files calculate genotypes ("0/0", "0/1", "1/1") for both concordant samples and check if one of the samples contains stretches of "0/0" and "1/1" while the other doesn't - this should be your tumor sample. 2) using Conpair estimate contamination for both combinations (1) sample A as tumor and sample B as normal 2) sample A as normal and sample B as tumor) and check if one of the combinations gives you a low contamination value - this should be the correct combination.

Hope this helps!