MarkDuplicates

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JAY SINGH

• January 10, 2021 13:41

I have sorted my bam file by query name. what should be the --ASSUME_SORTED option in MarkDuplicates.

In manual it is written about coordinate sorted bam file but not about query name sorted bam file.

Kindly give suggestion.

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  Genevieve Brandt (she/her)

  • January 11, 2021 21:57

  Hi JAY SINGH,

  Please see this tool documentation page for MarkDuplicates. --ASSUME_SORTED is deprecated, --ASSUME_SORT_ORDER is a better option to use.

  There is also a good explanation of the sort at the top of the page. 

  Hope this helps!

  Genevieve

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