Question: Phasing X chromosome variants using shapeit2
4.4 years ago by
rubic • 190
rubic • 190 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).
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