1. Technical Documentation
2. Troubleshooting GATK4 Issues
3. I am unable to use VQSR (recalibration) to filter variants

I'd like to suggest a tool that makes it easier to visualize the INFO and FORMAT fields that get computed in an unfiltered VCF. All the work that VQSR does is it "magically" shows the impact of thr...

• View comment
• Mike Keehan
• October 04, 2021 21:07
• 0 votes

1. Getting Started
2. Tutorials
3. (How to) Map and clean up short read sequence data efficiently

Hi Rachel, Are you aligning male fish or female fish?  Do X and Y in three spine stickleback  behave the same as mammals (cow,humans)? MarkDuplicates remove optical duplicates ie. remove multiple d...

• View comment
• Mike Keehan
• December 03, 2020 02:00
• 0 votes

1. Getting Started
2. Tutorials
3. (How to) Map and clean up short read sequence data efficiently

Dear GATK team I wonder if you could help me. I am following these best practices to produce alignments intended for structural variant calling. The recommended workflow suggests to change the PRIM...

• View comment
• Mike Keehan
• November 12, 2020 22:19
• 0 votes