Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
Aligned reads file
*.{bam, cram}
bai:file
(Optional) Aligned reads file index
*.{bai,crai}
meta2:map
Groovy Map containing reference information e.g. [ id:‘genome’ ]
fasta:file
Genome fasta file
*.{fa,fasta,fna}
meta3:map
fai:file
Genome fasta file index
*.{fai}
intervallist:file
Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList.
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.