Description

Produces comprehensive statistics from BAM file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

bai (file)

BAM/CRAM/SAM file index

*.{bai,crai,sai}

bait_intervals (optional file)

An interval list or bed file that contains the locations of the baits used.

baits.{interval_list,bed,bed.gz}

target_intervals (optional file)

An interval list or bed file that contains the locations of the targets.

targets.{interval_list,bed,bed.gz}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (optional file)

Reference fasta file

*.{fasta,fa,fna}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta_fai (optional file)

Reference fasta file index

*.{fasta,fa,fna}.fai

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta_dict (optional file)

Reference fasta sequence dictionary

*.{dict}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

coverage_metrics (file)

Alignment metrics files generated by picard CollectHsMetrics or CollectWgsMetrics

*_metrics.txt

multiple_metrics (file)

Alignment metrics files generated by picard CollectMultipleMetrics

*_{metrics}

versions (file)

File containing software versions

versions.yml
included in
rnadnavar
author
Github user matthdsm
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