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Phasing X chromosome variants using shapeit2
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15 months ago
rubic • 180
United States


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?


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