homopolymer, steps after alignment

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pingu

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Join Date: Jul 2015

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homopolymer, steps after alignment

10-05-2015, 07:13 AM

Hello.
I am implementing my pipeline and I have to start the steps after alignment. I have see on GATK pipeline that I have to do local realignment (indel realignment) but the problem of 454 Roche is the homopolymer, so I would like know if there is an other tool that I have to use.

Thank you in advance
Tags: gatk indelrealigner, homopolymer, my pipeline, roche 454

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