Description
Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data.
Input
Name (Type)
Description
Pattern
Target dataset in VCF/BCF format defined at all variable positions.
The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended).
*.{vcf,bcf,vcf.gz,bcf.gz}
Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20).
For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy.
chrXX:leftBufferPosition-rightBufferPosition