Hello, I have a problem where when using picard markduplicates i get the error: 'Value was put into PairInfoMap more than once' I grep out the read causing the issue because it (for some reason) has a duplicate readNAME. I rerun picard markduplicates and still get the error 'Value was put into PairInfoMap more than once'. This time however, it is because of a different duplicate read name.
I have analysed countless paired end data and never encounter this problem before.
My question: Is there a way to get a list of ALL the duplicated readnames so i can filter them all out?