remove CIGAR strings starting with insertion

Question

[drabiza1]

I'm trying to use mutato (https://github.com/annalam/mutato) to perform somatic variant calling on BAM files aligned with BWA.

mutato call --alt-reads=5 --alt-frac=0.05 hg19.fa sample.bam > variants.vcf

I get the follow error:

ERROR: CIGAR strings starting with insertion are not supported

What can I do to change the Bam file to avoid this error?

[seidel]

Have you tried asking the author? You might be able to use pysam to filter alignments based on CIGAR strings with insertions (cigarType == 1). You could also probably use bioalcidaejdk, which has methods for parsing CIGAR strings.

Answer 1

[cmdcolin]

I made a small program, kind of reverse engineered from mutato source code itself, that makes a new BAM file free of the "bad" CIGAR strings starting with insertion/deletion. it was fun to learn a little bit of rust to make this work https://github.com/cmdcolin/filter_cigars

i only briefly tested it but seemed like it worked on a basic CIGAR that I provided it with

maybe a fix could be applied to mutato source code directly, it could be worth reporting to them that tools like BWA output this type of thing naturally. that said, "insertions/deletions at the 0 position" seem more like they should be e.g. soft clipping. maybe you could check that you are using the latest bwa for example to see that this wasn't fixed in bwa.

[cmdcolin]

I see probably this may have been fixed already, but was a fun exercise nonetheless https://github.com/annalam/mutato/issues/1