Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Difference between GATK3.3 and GATK4.0

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    Anton Kovalsky

    Hi Daisy thanks so much for your question!

    When you say GATK4.0 are you specifically referring to GATK 4.0.0? If so, our first recommendation is that you update to the latest version, GATK 4.1.4.1

    However, there is a good chance that you will see a similar situation, as it is likely caused by some issue with LocalAssembly. We are currently working on some changes to HaplotypeCaller that might improve the assembly of these sites, and you can try some of our prototype code by running HaplotypeCaller with the --linked-de-bruijn-graph argument to see if it fixes the issue. If you try this, please let us know what you observe!

    You can also try running with the argument --debug-graph-transformations on while running on that subset of the genome where those variants were, so if you are still missing those variants, you can provide us with the dot files this argument outputs so we can take a closer look at why those variants are lost.

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