WGS Samples do not run Mark Duplicates

[DavidStreid]

Description: Since dragen-alignment marks duplicates, the Picard command isn't run that would output the .txt file that can be uploaded automatically to the LIMS.

Until this is added, the mark duplicate stats can be extracted from the DRAGEN metrics files written here - /igo/staging/stats/

E.g.
RUTH_0036_BHMJFKDSX2/RUTH_0036_BHMJFKDSX2___P09443_CM___116RO_T_IGO_09443_CM_3___GRCh38___HumanWholeGenome.mapping_metrics.csv

Extract the following stats from these *.csv files -

• Reads Examined
• Unmapped Reads
• Percent Duplication

$ cat /igo/staging/stats/RUTH_0036_BHMJFKDSX2/RUTH_0036_BHMJFKDSX2___P09443_CM___116RO_T_IGO_09443_CM_3___GRCh38___HumanWholeGenome.mapping_metrics.csv \
  | grep "MAPPING/ALIGNING SUMMARY,,Number of duplicate marked read"
MAPPING/ALIGNING SUMMARY,,Number of duplicate marked reads,463757354,15.38

[DavidStreid]

Will be addressed by - mskcc/ngs-stats#35