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.
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
UG outputs VCFs where different lanes from same sample are treated as separate individuals
We are running an exome sequencing project where we have sequenced samples on two different lanes. Aligning with bwa, we assign identical ID and SM tags, yet different PU tag for these files. This should be in line with your general recommendations, keeping the lane information available for recalibration purposes. We have then fed both files from the same sample into the base recalibration step to create a common, sample-level bam, also in accordance with recommendations previously posted on the forum. However, when calling variants we get VCFs where UnifiedGenotyper has treated the different lanes as separate samples. What are we doing wrong? Is this approach not possible after all, so an identical read group is required for each sample?