Lofreq subcommand to for insert base and indel alignment qualities
meta
:map
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
bam
:file
Sorted BAM/CRAM/SAM file
*.{bam,cram,sam}
fasta
Reference genome FASTA file
*.{fasta}
*.bam
BAM/CRAM/SAM file with base and indel alignment qualities
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
