Question: realignement around Indels
0
gravatar for Chadi Saad
2.3 years ago by
Chadi Saad60
France
Chadi Saad60 wrote:

Hello,

Is it possible to realign reads and force the aligner to put Indels at a certain position, instead of aligning reads to the left ? I found GATK realigner, but it demand an vcf file, while I have just the positions (without the REF / Alt fields in VCF).

alignment • 750 views
ADD COMMENTlink written 2.3 years ago by Chadi Saad60

Take a look at ABRA. It does realignments well.

ADD REPLYlink written 2.3 years ago by genomax74k

thanks, but how can I specify my prefered Indel Positions ? (Imagine I have an homopolymer of 5 A , with insertion of 1 A , and I need the aligner to put it in the middle of the homopolyper...)

ADD REPLYlink written 2.3 years ago by Chadi Saad60
1

If the realigner aligns all indels to the same position, why do you need it to be on a particular position? Any position will be arbitrary anyway.

ADD REPLYlink written 2.3 years ago by h.mon28k
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