Groovy Map containing sample information
e.g. [ id:‘test’ ]
bam
:file
Tumor sample sorted BAM file
*.{bam}
bai
:file
BAM index file
*.{bam.bai}
intervals
:file
BED file containing target regions for variant calling
*.{bed}
meta2
:map
Groovy Map containing sample information about the reference fasta
e.g. [ id:‘reference’ ]
fasta
:file
Reference genome FASTA file
*.{fasta}
meta3
:map
Groovy Map containing sample information about the reference fasta fai
e.g. [ id:‘reference’ ]
fai
:file
Reference genome FASTA index file
*.{fai}
Output
name:type
description
pattern
vcf
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz
:file
Predicted variants file
*.{vcf}
tbi
meta
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz.tbi
:file
Index of vcf file
*.{vcf.gz.tbi}
versions_lofreq
${task.process}
:string
Process which generated the version
lofreq
:string
Tool name
lofreq version | sed -n '1s/^.* //p'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
Process which generated the version
lofreq
:string
Tool name
lofreq version | sed -n '1s/^.* //p'
:eval
The expression to obtain the version of the tool
Tools
lofreq
MIT
Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors
