Question: Phasing X chromosome variants using shapeit2
gravatar for rubic
5.0 years ago by
United States
rubic200 wrote:


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 • 1.7k views
ADD COMMENTlink modified 4.9 years ago • written 5.0 years ago by rubic200
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