Caution
This repository is no longer maintained and the DNAnexus app code has been migrated into the Athena repository
DNAnexus app of Athena
Generates coverage reports to assess quality of NGS data.
Used to generate coverage reports to assess coverage of genomic regions defined in a bed file.
- Panel BED file
- Per base coverage BED file (output from mosdepth)
- Exons nirvana (exon annotation file; originally generated from Illumina Nirvana RefSeq gff file, analogous file can be created by following instructions here)
n.b. check Athena readme for required formats of input files, specific formatting is required and if not correct will result in errors / empty files being generated.
- thresholds: thresholds at which to calculate coverage (default: 10, 20, 30, 50, 100)
- build: text file containing reference build used for alignment (as output from eggd_mosdepth)
- name: sample name, used to name output files and within report title. If not given this will be parsed from the per base coverage bed.
- cutoff threshold: threshold at which to define sub-optimal coverage (must be one of the threshold values; default: 20)
- snps: VCF(s) of SNPs for which to calculate coverage for (i.e. HGMD, ClinVar)
- limit: number of genes in panel at which to not generate full gene plots, for large panels this may take a long time and will result in larger output report file size.
- panel: boolean option to display panel used in report (default: True)
- summary: boolean option to include summary of genes / transcripts used in report (default: False)
- per_chromosome_coverage: boolean option to include global per-chromosome coverage plots in report (default: False)
- {sample_name}_coverage_report.html: coverage report for sample.
- {sample_name}_exon_stats.tsv: contains per exon coverage metrics, used for generating report.
- {sample_name}_gene_stats.tsv: contains per gene coverage metrics, used for generating report.
- {sample_name}_annotated.bed: raw annotated bed file, contains per base coverage data.