How can I right align InDels ?

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6.8 years ago

Chadi Saad ▴ 100

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

for example

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

alignment • 2.1k views

ADD COMMENT • link updated 6.6 years ago by Biostar 20 • written 6.8 years ago by Chadi Saad ▴ 100

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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?

ADD REPLY • link 6.8 years ago by Rohit ★ 1.5k

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

ADD REPLY • link 6.8 years ago by Pierre Lindenbaum 161k

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

ADD REPLY • link 6.8 years ago by Chadi Saad ▴ 100

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...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.

ADD REPLY • link 6.6 years ago by Kevin Blighe 87k

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