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dnanexus-archive / viral-ngs

viral-ngs
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Additional reporting #59

Open tomkinsc opened 7 years ago

tomkinsc commented 7 years ago

Generate second coverage report with different options: Currently bedtools genomecov is used to create coverage reports for aligned bam files. This is great, but it would be helpful to also have a second coverage report with per-base depth information. This would be a matter of adding a second call here with the -d flag specified (bedtools docs).

Other metrics to report: Along with the other metrics collected, it would be helpful to report median coverage depth, assembly length fraction (relative to the reference genome), and % unambiguous bases of the assembly (relative to the reference genome).

tomkinsc commented 7 years ago

A PR is pending in the main viral-ngs repository to expose Picard's CollectIlluminaLaneMetrics. Once it has been merged in, it would be helpful to have the lane metrics report created alongside the barcodes report with a call to ./illumina.py lane_metrics