Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

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

GenomicsDBImport Follow

2 comments

  • Avatar
    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 (4.1.5.0), as increasing the amount of nodes does not affect computation time.

    0
    Comment actions Permalink
  • Avatar
    Jigdor

    Hello, I am using GenomicsDBImport and selectVariants (gatk/4.2.0.0) 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?

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk