Haplotype Phasing

agel · 01-11-2012, 01:57 PM

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)?

agel · 01-12-2012, 08:42 AM

Samtools has a phase function, but I can't seem to find how it works. Is it only read-based?

ymc · 01-14-2012, 12:32 AM

I want to know too. I only have SNP phasing experience..

agel · 01-16-2012, 12:02 PM

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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01-11-2012, 01:57 PM	#1
agel Junior Member Location: USA Join Date: Dec 2011 Posts: 5	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)?

01-12-2012, 08:42 AM	#2
agel Junior Member Location: USA Join Date: Dec 2011 Posts: 5	Samtools has a phase function, but I can't seem to find how it works. Is it only read-based?

01-14-2012, 12:32 AM	#3
ymc Senior Member Location: Hong Kong Join Date: Mar 2010 Posts: 498	I want to know too. I only have SNP phasing experience..

01-16-2012, 12:02 PM	#4
agel Junior Member Location: USA Join Date: Dec 2011 Posts: 5	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?