BBMap plus FreeBayes - only SNP calls, no indels

[HESmith]

I'm benchmarking combinations of aligners plus variant callers for mutation identification, and observed an unexpected output using BBMap plus FreeBayes. Only SNPs are reported in the VCF, even though the data contain indels. It's specific for this combination: BBMap plus SAMtools or GATK calls indels, as does BWA plus FreeBayes. I suspect that it's related to the difference in how the indel is represented in the BAM file:

BBMap example:
7395420_chr1_1_10552910_10552959_10544910_I 16 I 10545178 35 41=1D9=

BWA example:
7395420_chr1_1_10552910_10552959_10544910_I 16 I 10545178 37 41M1D9M

Just wanted to make the community aware of this issue.

-Harold

[Brian Bushnell]

I wonder if it's due to the "=" symbols in the sam file? You can turn those off (in BBMap) with the flag "sam=1.3". But, I'll contact The FreeBayes team. Thanks for noticing this!

[HESmith]

Thanks for the prompt reply, Brian. I'll rerun the pipeline with the recommended flag and report on the output.

-Harold

[HESmith]

The sam=1.3 flag fixed the problem - plenty of indels reported now. Thanks again, Brian!