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!
I have a simple question, followed by more info below if needed:
What have you been using for phasing your CGI data?
------------
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!