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Old 02-25-2014, 07:35 AM   #1
Sarutahiko
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Location: SouthEast

Join Date: Nov 2013
Posts: 5
Default Phasing Programs for CGI whole genomes

Hi everyone,

I have a simple question, followed by more info below if needed:

What have you been using for phasing your CGI data?

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Background:

I have a fairly large cohort of Whole Genomes sequenced by CGI.

We have ~90 African Americans and ~30 European Americans.

There are a lot of programs that can phase NGS data, but I was wondering if the community of people working specifically with CGI-sequenced data have converged on either:

1. a best software for this, especially if one has the luxury of a larger cohort
2. a way to do this for CGI BAM files, since they are slightly different

Am I correct in assuming that most software programs will not handle CGI BAMs correctly? If this is the case, can a VCF be used instead? Is there anything like acceptance of a best software here?

Thank you!
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