Question: How can I right align InDels ?
0
gravatar for Chadi Saad
15 months ago by
Chadi Saad50
France
Chadi Saad50 wrote:

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

for example

 ACGT**A**AAACGTA  -->  ACGTAAA**A**CGTA
alignment • 557 views
ADD COMMENTlink modified 13 months ago by Biostar ♦♦ 20 • written 15 months ago by Chadi Saad50
1

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 REPLYlink written 15 months ago by Rohit1.3k

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

ADD REPLYlink written 15 months ago by Pierre Lindenbaum112k

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

ADD REPLYlink written 15 months ago by Chadi Saad50

...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 REPLYlink modified 13 months ago • written 13 months ago by Kevin Blighe30k
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