Tool to create a binary reference panel for quick reading time.
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reference{:bash}
:file
Reference panel of haplotypes in VCF/BCF format.
*.{vcf.gz,bcf.gz}
reference_index{:bash}
Index file of the Reference panel file.
*.{vcf.gz.csi,bcf.gz.csi}
input_region{:bash}
:string
Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000).
chrXX:leftBufferPosition-rightBufferPosition
output_region{:bash}
Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000).
map{:bash}
File containing the genetic map.
*.gmap
bin_ref{:bash}
*.bin{:bash}
binary reference panel
*.bin
versions_glimpse2{:bash}
${task.process}{:bash}
The name of the process
glimpse2{:bash}
The name of the tool
GLIMPSE2_split_reference --help | grep -oE 'v[0-9.]+' | cut -c2-{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies.
