Does Markduplicates Work If Mate Pair Information Is Not 'Fixed'?

Question

[ian.streeter]

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.

Answer 1

[Johan]

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