Description

Converts certain output formats to VCF

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

The input format. Each format needs a seperate parameter to be specified in the args:

  • GEN/SAMPLE file: --gensample2vcf
  • gVCF file: --gvcf2vcf
  • HAP/SAMPLE file: --hapsample2vcf
  • HAP/LEGEND/SAMPLE file: --haplegendsample2vcf
  • TSV file: --tsv2vcf
*.{gen,sample,g.vcf,hap,legend}{.gz,}

input_index (file)

(Optional) The index for the input files, if needed

*.bed

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

(Optional) The reference fasta, only needed for gVCF conversion

*.{fa,fasta}

bed (file)

(Optional) The BED file containing the regions for the VCF file

*.bed

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

vcf_gz (file)

VCF merged output file (bgzipped) => when --output-type z is used

*.vcf.gz

vcf (file)

VCF merged output file => when --output-type v is used

*.vcf

bcf_gz (file)

BCF merged output file (bgzipped) => when --output-type b is used

*.bcf.gz

bcf (file)

BCF merged output file => when --output-type u is used

*.bcf

hap (file)

hap format used by IMPUTE2 and SHAPEIT

*.hap.gz

legend (file)

legend format used by IMPUTE2 and SHAPEIT

*.legend.gz

sample (file)

sample format used by IMPUTE2 and SHAPEIT

*.samples

Tools

bcftools
GPL

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.