Left-aligning indels

[genec]

I was under the impression that the GATK IndelRealigner was supposed to left-align indels. I know that GATK has LeftAlignIndels and LeftAlignVariants, but those both output vcf files, and I would like an adjusted left-aligned bam file.

Attached is an example where two different deletion calls should clearly be collapsed into just one deletion. This alignment is after running GATK IndelRealigner.

Are there any other tools that can left-align indels in a bam file?

[adaptivegenome]

The only other local realignment tool I know of is SRMA.

[nilshomer]

How good are you at coding? There are some functions already implemented that do this, but you would need to write the wrapper code or adapt them (they are in C/Java or something that isn't perl/python).

[gaffa]

Check out the 'bamleftalign' utility which comes with the FreeBayes SNP caller, it should do this.

[ekg]

I don't have the input data available, but this is exactly the kind of thing which bamleftalign is designed to resolve. Did it work for you?