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Collect MarkDuplicatesSpark metrics with the standalone Picard tool EstimateLibraryComplexity #81

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maxulysse opened this issue Dec 17, 2019 · 1 comment

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maxulysse commented Dec 17, 2019

cf #64
cf https://software.broadinstitute.org/gatk/documentation/tooldocs/current/org_broadinstitute_hellbender_tools_spark_transforms_markduplicates_MarkDuplicatesSpark.php

Collecting duplicate metrics slows down performance and thus the metrics collection is optional and must be specified for the Spark version of the tool with '-M'. It is possible to collect the metrics with the standalone Picard tool EstimateLibraryComplexity.

maxulysse self-assigned this

maxulysse added the enhancement label

maxulysse added this to the 3.0 milestone

FriederikeHanssen self-assigned this

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FriederikeHanssen commented Jul 15, 2021

Addressed in PR #388

FriederikeHanssen closed this as completed

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