Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read.
meta
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam
BAM file containing reads to be deduplicated via UMIs.
*.{bam}
bai
BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input.
*.{bai}
mode
Selects the mode of Umicollapse - either fastq or bam need to be provided.
{fastq,bam}
BAM file with deduplicated UMIs.
log
A log file with the deduplication statistics.
*_{UMICollapse.log}
versions
File containing software versions
versions.yml
UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs).
