wi-gatk release-report

[danielecook]

Similar to the alignment report (#117) , a report should be generated using the multiqc output from AndersenLab/wi-gatk.

The multiqc datasets are:

multiqc_sources.json
multiqc_bcftools_stats.json
multiqc_data.json
multiqc_general_stats.json
multiqc_qualimap_bamqc_genome_results.json
multiqc_snpeff.json

I will convert these to csv to make them easier to work with. I will also add metrics at the strain level (currently all are aggregate).

All graphs and data should be looked at in aggregate and on a strain-level.

Examples:

• Total number of strains, etc.
• # of SNPs
• # of Indels
• # of MNPs
• Distribution of predicted effects
• TS/TV ratios