Calls consensus sequences from reads with the same unique molecular tag.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, collapse:false ]
grouped_bam
:file
The input SAM or BAM file, grouped by UMIs
*.{bam,sam}
min_reads
:integer
Minimum number of original reads to build each consensus read.
min_baseq
Ignore bases in raw reads that have Q below this value.
bam
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.bam
Output SAM or BAM file to write consensus reads.
versions_fgbio
${task.process}
:string
The process the versions were collected from
fgbio
The tool name
fgbio --version 2>&1 | tr -d "[:cntrl:]" | sed -e "s/^.*Version: //;s/\[.*$//"
:eval
The expression to obtain the version of the tool
versions
Tools for working with genomic and high throughput sequencing data.
