modules/shapeit5_phaserare
Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).
Require feature AVX2.
phasingrare variantshaplotypeshapeit
Description
Tool to phase rare variants onto a scaffold of common variants (output of phase_common / ligate).
Require feature AVX2.
Input
Name (Type)
Description
Pattern
Index file of the input_plain VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
Region to be considered in --input-plain (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
Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20).
chrXX:leftBufferPosition-rightBufferPosition