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Old 01-11-2012, 01:57 PM   #1
agel
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Default Haplotype Phasing

I would like to phase whole-genome datasets, some of which are single-end read datasets and some of which are paired-end datasets. Does anyone have experience with this? Should I simply generate a list of SNPs and feed it to existing phasing algorithms? Is there software that can take the raw read data into account (IE SNPs that appear on the same read)?
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Old 01-12-2012, 08:42 AM   #2
agel
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Samtools has a phase function, but I can't seem to find how it works. Is it only read-based?
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Old 01-14-2012, 12:32 AM   #3
ymc
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I want to know too. I only have SNP phasing experience..
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Old 01-16-2012, 12:02 PM   #4
agel
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I have been unable to determine how samtools phase works. Is there a mailing list or email address of one of the writers I can ask?
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