realignement around Indels

Question

[Chadi Saad]

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).

[GenoMax]

Take a look at ABRA. It does realignments well.

[Chadi Saad]

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...)

[h.mon]

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.