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.
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!
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