We are doing targeted resequencing to detect rare variants in tumor samples using SOLiD with bfast as the front end of our analysis pipeline. We have found that occurrences of two (or even three) base changes in a row are very frequent in highly mutated samples, but unlike SNPs, bfast turns them back into reference sequence. The paper says it is easy to modify the code to deal with this issue and I think I know in principle what to do - I am wondering if anyone has done so and could send me a tip or two on where to look and how to proceed?
Thanks!
Thanks!
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