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

Using GenomicsDB with intervals

0

2 comments

  • Avatar
    Bhanu Gandham

    Hi ,

    The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

    Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

    We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

    For context, check out our support policy.

     

    0
    Comment actions Permalink
  • Avatar
    Jay Ross

    You can run GenomicsDBimport per chromosome, or on intervals smaller than whole chromosomes (I use an intervals list split anywhere there are consecutive N's in the reference genome). This will create a number of genomicDBs, which can then be genotyped into VCF files using GenotypeGVCFs. If all of the genomicsDB and VCF files have the same samples, you can then combine all VCF files into one final VCF using GatherVCFs.

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk