How can I align all indels to the right in Bam file ?
ACGT**A**AAACGTA --> ACGTAAA**A**CGTA
Is there a particular reason that last of the A in the homopolymer is pushed in the middle of the indel and the indels are not clustered together?
I might be naive, wouldn't the moving of the indels remove all the sense from the alignment. I wouldn't change the alignments without looking into the reference, so why not use a mapper that is homopolymer aware or with that particular error profile?
why right when there there is LeftAlignIndel https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_LeftAlignIndels.php ?
I need it in order to count InDels afters homopolymers (since they are aligned to the left by aligners)
...but should you even trust indels that are called around homopolymers? From my experience, these vanish from the VCF if you raise the MAPQ threshold to 50 or 60.