If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
Notice: Bug affecting ReduceReads -- GATK versions 2.0 and 2.1
We have identified a major bug in ReduceReads -- GATK versions 2.0 and 2.1. The effect of the bug is that variant regions with more than 100 reads and fewer than 250 reads get downsampled to 0 reads.
This has now been fixed in the most recent release.
To check if you are using a buggy version, run the following:
samtools view -H $BAM
This will produce the following output:
@PG ID:GATK ReduceReads VN:XXX
If XXX is 2.0 or 2.1, any results obtained with your current version are suspect, and you will need to upgrade to the most recent version then rerun your processing.
Our most sincere apologies for the inconvenience.