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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.
Attention:
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!

more reads in bamout file

Hi GATK team,
I'm using GATK v3.4 to call SNPs from RNA-Seq data. I generated a bamout file and viewed it in IGV, I expected to see the same or lower number of reads in the bamout file, but, strangely, I saw a lot of cases with higher reads in bamout than in the orignial. Do you know why this is happening? Thank you in advance!

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