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

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    Jonathan Klonowski

    Hello, I am trying to run GenomicsDbImport. Is this compatible with "-XX:+UseParallelGC -XX:ParallelGCThreads=4” I am asking because it seems that the command is restricted to a single node (, as increasing the amount of nodes does not affect computation time.

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    Hello, I am using GenomicsDBImport and selectVariants (gatk/ to combine gVCFs (results of haplotypecaller) of 45 samples. At an individual sample gVCF, I see that none of the GTs are missing ("./.") but after I run GenomicsDBImport and then SelectVariants, I see that all samples' GTs in the combined gVCFs are set to "./.". Alternately, I tried using combineGVCFs and I get the same "./." in the combinedgVCF. The log file  shows everything perfect without a single warning. What could be going wrong?

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