Locate and tag duplicate reads in a BAM file
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
reads:file
Sequence reads file, can be SAM/BAM/CRAM format
*.{bam,cram,sam}
meta2:map
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta:file
Reference genome fasta file, required for CRAM input
*.{fasta,fa}
meta3:map
fai:file
Reference genome fasta index
*.{fai}
bam
*.bam:file
BAM file with duplicate reads marked/removed
*.{bam}
bai
*.bai:file
An optional BAM index file. If desired, —CREATE_INDEX must be passed as a flag
*.{bai}
cram
*.cram:file
Output CRAM file
*.{cram}
metrics
*.metrics.txt:file
Duplicate metrics file generated by picard
*.{metrics.txt}
versions
versions.yml:file
File containing software versions
versions.yml
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
