can not find/display variants which observed in IGV

[asaki1986]

Hi,

Thanks for providing mutscan, which is fast enough to generally find the mutations.

However, I find it hard to display the variants that are already observed in IGV, mapped using raw reads. There are 10000x reads for wild-type, and 11 (6+, 5-) for mutant allele.

It will be great if you can share some experience.

Thanks

[yanlinlin82]

it would be easier to find the problem if you provide some minimum demo data to reproduce your case. I guess low base/mapping quality, orphan read, and too much depth could be common reasons.

[asaki1986]

Thanks for the reply. I upload the demo data which was extracted from my case, so that you can take a look.

GW9B0164B05.T790M.zip