Question: Phasing X chromosome variants using shapeit2
1
gravatar for rubic
3.2 years ago by
rubic180
United States
rubic180 wrote:

Hi,

 
I'm trying to phase X chromosome variants for several individuals using shapeit2 using the 1000 Genomes Project Phase3 chrX haplotypes as a reference set. My data consist of a VCF file for each individual which was generated using GATK from the whole-exome-sequencing, so I also have the corresponding bam files.
 
I followed the example on shapeit's webpage on how to phase chrX variants with the example data they provide in the shapeit package but it produces zero phased X variants (the output.haps file is empty).

Any idea?

 
 
sequencing snp next-gen • 1.2k views
ADD COMMENTlink modified 3.1 years ago • written 3.2 years ago by rubic180
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