Input
Either multiple BAM/CRAM files containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods.
When using BAM/CRAM the name of the file is used as samples name.
*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}
Index file of the input BAM/CRAM/VCF/BCF file.
*.{bam.bai,cram.crai,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).
Optional if reference panel is in bin format.
chrXX:leftBufferPosition-rightBufferPosition
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
Optional if reference panel is in bin format.
chrXX:leftBufferPosition-rightBufferPosition
Faidx-indexed reference sequence file in the appropriate genome build.
Necessary for CRAM files.
*.fasta