Description

Ligate multiple phased BCF/VCF files into a single whole chromosome file. Typically run to ligate multiple chunks of phased common variants.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

input_list (file)

VCF/BCF files containing genotype probabilities (GP field).
The files should be ordered by genomic position.

*.{vcf,bcf,vcf.gz,bcf.gz}

input_list_index (file)

VCF/BCF files index.

*.csi

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

merged_variants (file)

Output VCF/BCF file for the merged regions.
Phased information (HS field) is updated accordingly for the full region.

*.{vcf,bcf,vcf.gz,bcf.gz}
included in
phaseimpute
maintainer
Github user louislenezet
get in touch
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