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varfish-cli tools dragen-to-bam-qc fails with current Dragen output #131

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Nicolai-vKuegelgen opened this issue Sep 27, 2024 · 0 comments · Fixed by #134
Closed

varfish-cli tools dragen-to-bam-qc fails with current Dragen output #131

Nicolai-vKuegelgen opened this issue Sep 27, 2024 · 0 comments · Fixed by #134
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@Nicolai-vKuegelgen
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Describe the bug
The varfish-cli tools dragen-to-bam-qc functionality should parse mapping_metrics and coverage_metrics csv files from dragen. However, with current/recent Dragen files, it fails to parse the mapping_metrics.csv files.
The main issue is that the 'Insert length: mean' (as well as median and standard devaition) field occurs more than once in the mapping_metrics.csv file (this might have not been the case in the past), and some entries are NA and can not be parsed.
Additionally it seems like the current code also only looks at the 3rd column of the metrics file to differentiate values, however specifically the 'Insert length: mean' values are also differentiated by the first two columns ("MAPPING/ALIGNING SUMMARY" vs "MAPPING/ALIGNING PER RG"; and "", "WGS", "EvidenceRead_Normal" and "EvidenceHaplotype").

Current dragen version: "07.021.624.3.10.15"

To Reproduce
I can provide current dragen input files on request.

Steps to reproduce the behavior:

  1. Run varfish-cli tools dragen-to-bam-qc with current dragen *mapping_metrics.csv files included in the input
  2. See error:
    [E 240925 14:46:05] 'Insert length: mean' not in [...].mapping_metrics.csv or no int

Expected behavior
Current mapping_metrics.csv files should be parsable. Either the dragen-to-bam-qc tools needs to be able to handle NA values reported by dragen, or - more likely - it needs to select the correct 'Insert length: mean' value fields from the file.

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