Tool for imputation and phasing from vcf file or directly from bam files.
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
input:file
Either one or multiple BAM/CRAM files in an array 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}
input_index:file
Index file of the input BAM/CRAM/VCF/BCF file.
*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}
bamlist:file
File containing the list of BAM/CRAM files to be phased.
One file per line and a second column can be added to indicate the sample name.
*.{txt,tsv}
samples_file:file
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}
input_region:string
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
output_region:string
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
Optional if reference panel is in bin format.
chrXX:leftBufferPosition-rightBufferPosition
reference:file
Reference panel of haplotypes in VCF/BCF format.
*.{vcf.gz,bcf.gz}
reference_index:file
Index file of the Reference panel file.
*.{vcf.gz.csi,bcf.gz.csi}
map:file
File containing the genetic map.
Optional if reference panel is in bin format.
*.gmap
meta2:map
Groovy Map containing genomic map information
e.g. [ map:'GRCh38' ]
fasta_reference:file
Faidx-indexed reference sequence file in the appropriate genome build.
Necessary for CRAM files.
*.fasta
fasta_reference_index:file
Faidx index of the reference sequence file in the appropriate genome build.
Necessary for CRAM files.
*.fai
Output
name:type
description
pattern
phased_variants
meta:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.{vcf,vcf.gz,bcf,bgen}:file
Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score.
*.{vcf,bcf,vcf.gz,bcf.gz}
stats_coverage
meta:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.txt.gz:file
Optional coverage statistic file created when BAM/CRAM files are used as inputs.
*.txt.gz
versions
versions.yml:file
File containing software versions
versions.yml
Tools
glimpse2
MIT
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
