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How can I right align InDels ?
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23 months ago
Chadi Saad • 60
France

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

for example

 ACGT**A**AAACGTA  -->  ACGTAAA**A**CGTA
alignment • 813 views
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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?

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

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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.

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