Question: Haplotype resolving (phasing) from BAM file
gravatar for greentailedmouse
4.4 years ago by
greentailedmouse50 wrote:

Hi all,

I have a question about what I first thought would be a trivial task. I would like to resolve the haplotypes of a non-model (diploid) species. I have a genome assembly, and a bam file where the reads (that were used for genome assembly) are mapped. The genotype of the mapped reads is thus the same as the "reference" genome, I just want to properly resolve the two haplotypes.

Since the genome assembly is by definition a chimera of both haplotypes I cannot just take the assembly as a reference and call SNPs (which I would do with haplotypeCaller from GATK). I tried using samtools phase (which sounded like the perfect solution for the problem) but I have a hard time interpreting the output file so I am not even sure if this is what I'm looking for, especially since some SNPs are clearly missed in the output and some seem to be sorted incorrectly.

I'm unlikely the first person to try to do this (even though I cannot find any similar questions on BioStars), so my question is - which tools do you use to phase/resolve haplotypes?

bam haplotype • 2.3k views
ADD COMMENTlink written 4.4 years ago by greentailedmouse50

Hello greenttailedmouse, Did you solve the problem in the meantime? I have the same request...could you help me?

ADD REPLYlink written 3.8 years ago by chiaraunivpm0

Hi, Did you solve the problem?

ADD REPLYlink written 22 months ago by Peter Chung120

Another member with the same problem, did you solve it?

ADD REPLYlink written 9 months ago by gubrins60

almost 4 years, I think he is still working on it, lets be patient

ADD REPLYlink written 9 months ago by Peter Chung120
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