Phasing X chromosome variants using shapeit2

Question

[rubic]

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?