Lofreq subcommand to call low frequency variants from alignments
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
BAM input file
*.{bam}
intervals
BED file containing target regions for variant calling
*.{bed}
fasta
The reference fasta file
vcf
*.vcf.gz
VCF output file
*.{vcf}
versions_lofreq
${task.process}
:string
Process which generated the version
lofreq
Tool name
lofreq version | sed -n '1s/^.* //p'
:eval
The expression to obtain the version of the tool
versions
A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data
