modules/bcftools_convert

Converts certain output formats to VCF

bcftoolsconvertvcfgvcf

https://github.com/nf-core/modules/[...]/modules/nf-core/bcftools/convert

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:false ]

`input:file`

The input format. Each format needs a separate 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

`vcf_gz`

`meta:map`

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

`*.vcf.gz:file`

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

*.vcf.gz

`vcf`

`meta:map`

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

`*.vcf:file`

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

*.vcf

`bcf_gz`

`meta:map`

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

`*.bcf.gz:file`

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

*.bcf.gz

`bcf`

`meta:map`

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

`*.bcf:file`

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

*.bcf

`hap`

`meta:map`

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

`*.hap.gz:file`

hap format used by IMPUTE2 and SHAPEIT

*.hap.gz

`legend`

`meta:map`

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

`*.legend.gz:file`

legend format used by IMPUTE2 and SHAPEIT

*.legend.gz

`samples`

`meta:map`

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

`*.samples:file`

samples format used by IMPUTE2 and SHAPEIT

*.samples

`tbi`

`meta:map`

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

`*.tbi:file`

Alternative VCF file index

*.tbi

`csi`

`meta:map`

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

`*.csi:file`

Default VCF file index

*.csi

`versions`

`versions.yml:file`

File containing software versions

versions.yml

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.

samtools.github.io/bcftools/bcftools samtools.github.io/bcftools/bcftools.html#convert https://github.com/samtools/bcftools 10.1093/gigascience/giab008

modules/bcftools_convert

Description

Input

meta:map

input:file

input_index:file

meta2:map

fasta:file

bed:file

Output

vcf_gz

meta:map

*.vcf.gz:file

vcf

meta:map

*.vcf:file

bcf_gz

meta:map

*.bcf.gz:file

bcf

meta:map

*.bcf:file

hap

meta:map

*.hap.gz:file

legend

meta:map

*.legend.gz:file

samples

meta:map

*.samples:file

tbi

meta:map

*.tbi:file

csi

meta:map

*.csi:file

versions

versions.yml:file

Tools

bcftools GPL

`meta:map`

`input:file`

`input_index:file`

`meta2:map`

`fasta:file`

`bed:file`

`vcf_gz`

`meta:map`

`*.vcf.gz:file`

`vcf`

`meta:map`

`*.vcf:file`

`bcf_gz`

`meta:map`

`*.bcf.gz:file`

`bcf`

`meta:map`

`*.bcf:file`

`hap`

`meta:map`

`*.hap.gz:file`

`legend`

`meta:map`

`*.legend.gz:file`

`samples`

`meta:map`

`*.samples:file`

`tbi`

`meta:map`

`*.tbi:file`

`csi`

`meta:map`

`*.csi:file`

`versions`

`versions.yml:file`

bcftools
GPL