FDA TOTAL_READS confusion

[evelyn-schmidt]

Kelsy noticed that there seems to be some incorrect values in the FDA quality threshold report. The TOTAL_READS for both tumor DNA, normal DNA, and RNA was extremely low and prompted suspicion as to why that number was so low. The number comes from the unaligned_metrics1.txt and is the total reads for only one read fastq. The fda metrics script pulls the number from the unaligned_tumor_table. In the other fda metrics files, the label total reads is the combined read1 and read2 number of reads. So initially this value in the FDA metrics report is misleading and appears to be incorrect. However, @malachig clarified that the TOTAL_READS should indeed be the total reads for one read file.

• I suggest renaming TOTAL_READS to be something more clear so this confusion does not happen in the future
  • maybe TOTAL_READS_R1
• I also suggest adding the file paths to scripts/fda_quality_thresholds.csv so that it is clear where thes values are being pulled from
• Finally, I think t would be helpful if the qc report has the evaluation label on the metrics so one did not have to references the neoantigen design doc when writing the final report