Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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

Sign In or Register to comment.