modules/glimpse_phase
main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods
phaseimputationlow-coverageglimpse
Input
Name (Type)
Description
Pattern
Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
File with sample names and ploidy information.
One sample per line with a mandatory second column indicating ploidy (1 or 2).
Sample names that are not present are assumed to have ploidy 2 (diploids).
GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy.
*.{txt,tsv}
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition