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Log and evaluate PCT_PF_READS_IMPROPER_PAIRS #2052

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jemten opened this issue Sep 27, 2023 · 1 comment
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Log and evaluate PCT_PF_READS_IMPROPER_PAIRS #2052

jemten opened this issue Sep 27, 2023 · 1 comment

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@jemten
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jemten commented Sep 27, 2023

From slack conversation with @karlnyr

There is a need to log the metric PCT_PF_READS_IMPROPER_PAIRS that is generated by picard CollectMultipleMetrics. The metric is in the file <prefix>_collectmultiplemetrics.alignment_summary_metrics. Furthermore it would help if MIP failed in analysisrunstatus for samples going above the threshold 5%.
This was referenced Oct 4, 2023
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jemten commented Oct 9, 2023

done in #2054

@jemten jemten closed this as completed Oct 9, 2023
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