Trouble with GATK due to Cigar representation

Question

Closed this issue 9 years ago · 2 comments

Hi,

I just found out that for some reads right right after a deletion, Cigar information is changed. (Ex. 149M > 16D149M)

In aligned bam
M00288:85:000000000-A96N9:1:1103:13423:15386 163 chr17 7579660 70 149M = 7579755 244

In re-aligned bam
M00288:85:000000000-A96N9:1:1103:13423:15386 163 chr17 7579644 60 16D149M = 7579755

This causes some problems in GATK and MuTect. Would you please look into it?

Thanks,
Joon

Answer 1 · 2014-08-24T23:58:01.000Z

This issue can be resolved by using an optional argument "-rf BadCigar" while performing GATK base quality recalibration.

Joon

Answer 2 · 2014-08-25T13:42:49.000Z

Thanks for pointing this out along with the work around. I'll get a fix into an forthcoming release.