Collect metrics from a RNAseq BAM file
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false, strandedness:true ]
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
metrics
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
*.rna_metrics:file
RNA alignment metrics files generated by picard
*.rna_metrics
pdf
*.pdf:file
Plot normalized position vs. coverage in a pdf file generated by picard
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.
