Question: Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?
gravatar for ian.streeter
7.4 years ago by
ian.streeter10 wrote:

I would like to use the picard's MarkDuplicates to count the number of duplicates in a bam file. However, I have not yet run samtools fixmate to ensure that all mate-pair information is correct. Will this effect the output from MarkDuplicates? Does MarkDuplicates work even if mate pair information is not 'fixed'?

The bam file was produced with bwa and it has been sorted use picard SortSam.

ADD COMMENTlink modified 2.7 years ago by Biostar ♦♦ 20 • written 7.4 years ago by ian.streeter10
gravatar for Johan
7.4 years ago by
Johan870 wrote:

You should be able to run MarkDuplicates if you use the VALIDATION_STRINGENCY=LENIENT option.

ADD COMMENTlink modified 7.4 years ago • written 7.4 years ago by Johan870
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