Collects hybrid-selection (HS) metrics for a SAM or BAM file.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
An aligned BAM/CRAM/SAM file
*.{bam,cram,sam}
bai:file
Optional aligned BAM/CRAM/SAM file index
*.{bai,crai,sai}
bait_intervals:file
An interval file that contains the locations of the baits used.
*.{interval_list,bed,bed.gz}
target_intervals:file
An interval file that contains the locations of the targets.
meta2:map
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta:file
A reference file to calculate dropout metrics measuring reduced representation of reads. Optional input.
*.{fa,fasta,fna}
meta3:map
fai:file
Index of FASTA file. Only needed when fasta is supplied.
*.fai
meta4:map
dict:file
Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied.
*.dict
metrics
*_metrics:file
Alignment metrics files generated by picard
*_{metrics}
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.
