Coverage exon level

The table below shows which exons in each gene has sub-optimal coverage for each given threshold.

The above is also shown diagrammatically in the plots below. These plots are interactive allowing users to assess what portion of the exons has sub-optimal coverage

The summary section provides an overview of the report as seen below. Key information about the panel and coverage threshold and statistics are displayed. For example in this report the coverage threshold was set at 500X and the number of genes not covered 100% at 500X were 8.

The plot in the summary section diagrammatically illustrates which genes have an overall coverage above 99% (green), below 99% (yellow) and below 95% (red).

Coverage gene level

This section provides coverage metrics for each gene, showing which genes have sub-optimal coverage for a given threshold.

Users can optionally outpout coverage plots per exon for each gene.

The per exon coverage section provides coverage metrics for all exons in all genes.

The first section of the report provides an overview of all sections in the report and the sample name for each report.

The coverage per chromosome section provides an overview of the global read coverage per chromosome (target regions only for target-capture assays).

The following subpages serve to summarize each section of the athena coverage report.

The athena tool is made of 3 parts; 1) annotate the bed file 2) generate statistic files 3) generate the coverage report. This can be run independently or together with a single workflow:

Run independently:

1. Annotate each region of the bed file with the gene, exon and per base coverage data using https://github.com/msk-access/cwl-commandlinetools/blob/develop/athena/1.4.2/annotate_bed/annotate_bed.cwl

2. Generate per exon and per gene statistics using

3. Generate HTML coverage report with

Run three steps with a single workflow:

• Run all 3 steps above using a single workflow using

Coverage of known variants

Athena is a tool to generate coverage statistics for NGS data, and combine these into an interactive HTML report. This gives both summary level and in depth information as to the coverage of the data, including various tables and plots to visualise the data. Examples of the output statistics files and may be found in data/example. Athena can also optionally include plots visualising per-chromosome level coverage - refer to this for an example. More details can be found

Credits

Jethro Rainford - Cambridge University Hospital UK