Description

Filtering VCF with dynamically-compiled java expressions

Input

name:type
description
pattern

meta:map

Groovy Map containing VCF information e.g. [ id:‘test_reference’ ]

vcf:file

Input VCF/BCF file

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

tbi:file

Optional VCF/BCF index file

*.{tbi,csi}

regions_file:file

Optional. Restrict to regions listed in a file

*.{bed,bed.gz,txt,tsv}

meta2:map

Groovy Map containing fasta information e.g. [ id:‘test_reference’ ]

fasta:file

Fasta reference file

*.fasta

meta3:map

Groovy Map containing fasta.fai information e.g. [ id:‘test_reference’ ]

fai:file

Fasta file index

*.fasta.fai

meta4:map

Groovy Map containing fasta.dict information e.g. [ id:‘test_reference’ ]

dict:file

GATK sequence dictionary

*.dict

meta5:map

Groovy Map containing code information e.g. [ id:‘test_reference’ ]

code:file

File containing custom user code . May be empty if script if provided via task.ext.args2.

*.{code,script,txt,tsv,java,js}

meta6:map

Groovy Map containing pedigree information e.g. [ id:‘test_reference’ ]

pedigree:file

Optional jvarkit pedigree.

*.{tsv,ped,pedigree}

Output

name:type
description
pattern

vcf

meta:map

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

*.${extension}:file

VCF filtered output file

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

tbi

meta:map

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

*.tbi:file

Alternative VCF file index

*.tbi

csi

meta:map

Groovy Map containing VCF 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
MIT

View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF

args_id: $args1$args3
http://samtools.github.io/bcftools/bcftools http://www.htslib.org/doc/bcftools 10.1093/bioinformatics/btp352
maintainer
Github user lindenb
get in touch
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