Filtering VCF with dynamically-compiled java expressions
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
Optional VCF/BCF index file
*.{tbi,csi}
regions_file
Optional. Restrict to regions listed in a file
*.{bed,bed.gz,txt,tsv}
meta2
Groovy Map containing fasta information e.g. [ id:‘test_reference’ ]
fasta
Fasta reference file
*.fasta
meta3
Groovy Map containing fasta.fai information e.g. [ id:‘test_reference’ ]
fai
Fasta file index
*.fasta.fai
meta4
Groovy Map containing fasta.dict information e.g. [ id:‘test_reference’ ]
dict
GATK sequence dictionary
*.dict
meta5
Groovy Map containing code information e.g. [ id:‘test_reference’ ]
code
File containing custom user code . May be empty if script if provided via task.ext.args2.
task.ext.args2
*.{code,script,txt,tsv,java,js}
meta6
Groovy Map containing pedigree information e.g. [ id:‘test_reference’ ]
pedigree
Optional jvarkit pedigree.
*.{tsv,ped,pedigree}
Groovy Map containing VCF information e.g. [ id:‘test’, single_end:false ]
*.${extension}
VCF filtered output file
*.tbi
Alternative VCF file index
csi
*.csi
Default VCF file index
versions_jvarkit
${task.process}
:string
The name of the process
jvarkit
The name of the tool
jvarkit -v
:eval
The expression to obtain the version of the tool
versions_bcftools
bcftools
bcftools --version |& sed '1!d;s/bcftools //'
versions
Java utilities for Bioinformatics.
$args2
View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF
$args$args3
