Collects hybrid-selection (HS) metrics for a SAM or BAM file.
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
An aligned BAM/CRAM/SAM file
*.{bam,cram,sam}
bai
Optional aligned BAM/CRAM/SAM file index
*.{bai,crai,sai}
bait_intervals
An interval file that contains the locations of the baits used.
*.{interval_list,bed,bed.gz}
target_intervals
An interval file that contains the locations of the targets.
meta2
Groovy Map containing reference information e.g. [ id:‘genome’ ]
ref
A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input.
*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}
meta3
ref_fai
Index of reference file. Only needed when reference is supplied.
*.fai
meta4
ref_dict
Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.
*.dict
meta5
ref_gzi
Index of reference file. Only needed when gzipped reference is supplied.
*.gzi
metrics
*_metrics
Alignment metrics files generated by picard
*_{metrics}
versions_picard
${task.process}
:string
The process the versions were collected from
picard
The tool name
picard CollectHsMetrics --version 2>&1 | sed -n 's/.*Version://p'
The command used to generate the version of the tool
versions
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
