Concatenates imputation chunks in a single VCF/BCF file ligating phased information.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
input_list
:file
VCF/BCF file containing genotype probabilities (GP field).
*.{vcf,bcf,vcf.gz,bcf.gz}
input_index
Index file of the input VCF/BCF file containing genotype likelihoods.
*.{vcf.gz.csi,bcf.gz.csi}
merged_variants
Output VCF/BCF file for the merged regions. Phased information (HS field) is updated accordingly for the full region.
versions_glimpse
${task.process}
:string
The name of the process
glimpse
The name of the tool
GLIMPSE_ligate --help | sed -n '/Version/s/.*: //p'
:eval
The expression to obtain the version of the tool
versions
GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies.
