I've got an error using Picard MarkDuplicates function. It worked fine on my data before I add an other step in my pipeline, where I use samtools view -F4 -h to remove unmapped reads in the alignement. If I do this, an error occured during Picard treatment :
Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 6, Read name FCC63KDACXX:3:1115:14357:43781#GCGGAACT_TCTTTCCC, Mate unmapped flag should not be set for unpaired read.
Do you have any ideas of how to fix that ? I understand the error but I don't know how to make it works. Previously I 'manually' removed unmapped reads (reads for which an * appears in the 3rd column in the sam files) but I read that's not the good way to do that and that the best way is to use samtools with the command line above.