Remove duplicate readnames from a bam file

Question

[garnerim1988]

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?

Bw, Ian.

[finswimmer]

Hello garnerim1988 ,

have you tried the things mentioned in Markduplicates: Value Was Put Into Pairinfomap More Than Once ?

Or here: https://gatkforums.broadinstitute.org/gatk/discussion/10115/picard-markdup-error-value-was-put-into-pairinfomap-more-than-once

fin swimmer

[Bastien Hervé]

I'll add this one

https://gatkforums.broadinstitute.org/gatk/discussion/7431/markduplicates-error-value-was-put-into-pairinfomap-more-than-once

[garnerim1988]

Hi fin swimmer, thank you for your reply. Both links I have previously read but i will go through them more thoroughly again. I did triplicates of ATAC-seq across a bunch of cell lines and for some i have no problems and others i do which is what is so frustrating.

[Istvan Albert]

filter your BAM files to contain only primary alignments - perhaps having the read reported with multiple alignments is the source of the problem.

[garnerim1988]

Have done this, still has the same Error.