support "male non-pseudoautosomal X-chromosome genotypes to be coded as homozygous diploid genotypes"

plantimals / 2vcf

convert 23andme or Ancestry.com raw genotype calls into VCF format, with dbSNP annotations

MIT License

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Closed plantimals closed 2 years ago

plantimals commented 5 years ago

In order to support using 2vcf output with Beagle imputation or phasing:

Beagle requires male non-pseudoautosomal X-chromosome genotypes to be coded as homozygous diploid genotypes

implement a command line option to allow users to generate beagle compatible VCFs