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Alright. Thanks for your response.
Hi Sheila and pdexheimer, Thanks very much for your replies. Shiela, what I was wondering is if it's possible to get the set of metrics found in the "duplication metrics" file produced by MarkDuplicates, but without having to run MarkDup…
Sorry, but that's not satisfactory for me. If you run the supposedly same program on the same data twice and get different results, I think there is reason to be concerned, unless the program is randomly sub-sampling the data to derive these metrics…
Thanks for the quick reply. Just ran EstimateLibraryComplexity on a bam that already went through MarkDuplicates, and got different results from the original duplication metrics. Should I be using non-default parameters?