How can I right align InDels ?

Question

[Chadi Saad]

How can I align all indels to the right in Bam file ?

for example

 ACGT**A**AAACGTA  -->  ACGTAAA**A**CGTA

[Rohit]

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?

[Pierre Lindenbaum]

why right when there there is LeftAlignIndel https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_gatk_tools_walkers_indels_LeftAlignIndels.php ?

[Chadi Saad]

I need it in order to count InDels afters homopolymers (since they are aligned to the left by aligners)

[Kevin Blighe]

...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.