Collect metrics from a RNAseq BAM file
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, strandedness:true ]
bam{:bash}
:file
BAM/SAM file
*.{bam,sam}
ref_flat{:bash}
Genome ref_flat file
fasta{:bash}
Genome fasta file
rrna_intervals{:bash}
Interval file of ribosomal RNA regions
metrics{:bash}
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.rna_metrics{:bash}
RNA alignment metrics files generated by picard
*.rna_metrics
pdf{:bash}
*.pdf{:bash}
Plot normalized position vs. coverage in a pdf file generated by picard
versions{:bash}
versions.yml{:bash}
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.
