Groovy Map containing sample information
e.g. [ id:‘test’ ]
bam{:bash}
:file
Tumor sample sorted BAM file
*.{bam}
bai{:bash}
:file
BAM index file
*.{bam.bai}
intervals{:bash}
:file
BED file containing target regions for variant calling
*.{bed}
meta2{:bash}
:map
Groovy Map containing sample information about the reference fasta
e.g. [ id:‘reference’ ]
fasta{:bash}
:file
Reference genome FASTA file
*.{fasta}
meta3{:bash}
:map
Groovy Map containing sample information about the reference fasta fai
e.g. [ id:‘reference’ ]
fai{:bash}
:file
Reference genome FASTA index file
*.{fai}
Output
name:type
description
pattern
vcf{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz{:bash}
:file
Predicted variants file
*.{vcf}
tbi{:bash}
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
*.vcf.gz.tbi{:bash}
:file
Index of vcf file
*.{vcf.gz.tbi}
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
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
