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updated the documentation to no longer contain a misleading usage example #5938

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May 14, 2019
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updated the documentation to no longer contain a misleading usage example #5938

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11 changes: 9 additions & 2 deletions .../broadinstitute/hellbender/tools/spark/transforms/markduplicates/MarkDuplicatesSpark.java
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Expand Up @@ -71,12 +71,19 @@
* </pre>
*
*
* MarkDuplicatesSpark run locally specifying the removal of sequencing duplicates and tagging OpticalDuplicates
* MarkDuplicatesSpark run locally specifying the removal of sequencing duplicates
* <pre>
* gatk MarkDuplicatesSpark \
* -I input.bam \
* -O marked_duplicates.bam \
* --remove-sequencing-duplicates
* </pre>
*
* MarkDuplicatesSpark run locally tagging OpticalDuplicates using the "DT" attribute for reads
* <pre>
* gatk MarkDuplicatesSpark \
* -I input.bam \
* -O marked_duplicates.bam \
* --remove-sequencing-duplicates \
* --duplicate-tagging-policy OpticalOnly
* </pre>
*
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