Just wondering if this is plausible...
I am working with head and neck squamous cell cancer samples from TCGA, and the tumors do not have any somatic mutations when I view it through IGV - specifically on TP53. Commonly there should be a high mutation rate for this cancer type.
I see common SNPs but no mutation. Could it be that part of the workflow removed them?
I simply trim adapters and poly-N and low quality (<10) reads. I then align it with STAR (assigning 60 MQ for unique mappers). I add RG info, mark duplicates, and split/trim N CIGAR (introns).
I've view the sample after alignment, after deduping, and after trimming N reads but in each case, there are no mutations...
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Thanks for the link. I tried querying for head and neck cancer but weirdly nothing shows up.
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umn_bist •
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Not sure how long this link will last but click on the mutations tab when the page loads.
Thanks for the link. I tried querying for head and neck cancer but weirdly nothing shows up.