Description

Collect metrics from a RNAseq BAM file

Input

name:type
description
pattern

meta:map

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

, strandedness
]

bam:file

BAM/SAM file

*.{bam,sam}

ref_flat:file

Genome ref_flat file

fasta:file

Genome fasta file

rrna_intervals:file

Interval file of ribosomal RNA regions

Output

name:type
description
pattern

metrics

meta:map

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

]

*.rna_metrics:file

RNA alignment metrics files generated by picard

*.rna_metrics

pdf

meta:map

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

]

*.pdf:file

Plot normalized position vs. coverage in a pdf file generated by picard

versions

versions.yml:file

File containing software versions

versions.yml

Tools

picard
MIT

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.