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samtools.SAMException: Value was put into PairInfoMap more than once

Please excuse my naivety but I am trying to call snps using the gatk-4.1.2.0/gatk-package-4.1.2.0-local.jar tool. The data I have come from gene panel, paired-end sequencing.
When the script executes MarkDuplicates to mark the duplicate sequence
./gatk4-BP2019-processing-for-variant-discovery.sh
i got an error (Captura de pantalla 2019-07-24 19.30.13.png).
I try to find a solution in our forums, but i failed. I have also tried the following:
Step 1) Checking the merged aligned and unmapped files (Captura de pantalla 2019-07-24 20.17.17.png).
Step 2) Try to fix Errors and Warnings with (picard.jar AddOrReplaceReadGroups) (Captura de pantalla 2019-07-24 20.17.17.png)
Step 3) Re-checking the merged aligned and unmapped files (Captura de pantalla 2019-07-24 20.26.58.png).

Can anyone tell me how to fix it?
Thanks a lot.

Answers

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