I have a question with calling indels with Pindel. First I use BWA mem in mapping the reads with hg19 reference with default parameter. Then I use pindel to call indels, since I have the standard answers of my data. The mutation rate of indels are all below the answers. I use 1% and 500X depth as a cut-off value. Therefore I missed some high confidence somatic indels (should be above 1% in mutation rate).
For now, we think that it may be the parameter we set in BWA mapping. Maybe we should change the mismatch settings to a lower one to allow more mismatch. Does anyone have encountered this situation and could give us some suggestions? It would be highly appreciated. Thank you for your time.