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realignement around Indels

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
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written by Chadi Saad Chadi Saad

Take a look at ABRA. It does realignments well.

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written by GenoMax GenoMax

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...)

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written by Chadi Saad Chadi Saad

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.

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written by h.mon h.mon

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