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How to call this insertion?
I am attempting to repeat the variant calling in a dataset that has already been analysed before. I have tried to call a specific insertion that produces a frame shift. However, I have not been able to call it using the UniversalGenotyper nor the SomaticIndelDetector. What might be the reason for this?
Changing parameters such as -dcov and -stand_emit_conf do appear to affect the sensitivity of SNP calling, but in this case they don't seem to help with Indel calling. What parameters could I adjust to get greater sensitivity here?
The coverage at the position is 54 with 13 reads that have the insertion.
(Two images of the insertion below.)