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

selectvariants error when consolidating GVCFs

Answered
0

3 comments

  • Avatar
    Pamela Bretscher

    Hi jingchun liu,

    It looks like the error is most likely coming from your command, in that the tool isn't recognizing your "trio-gdb" file as a GenomicsDB. Can you try using the gendb:// prefix to access the file? You can find information about the command specifications in the SelectVariants documentation. 

    Kind regards,

    Pamela

    0
    Comment actions Permalink
  • Avatar
    jingchun liu

    Pamela,

    Thank you so much! I thought gendb:// is just to tell the directory of the file. Now I know it tells gatk the file format and directory both.

    Kind regards,

    Jingchun

    0
    Comment actions Permalink
  • Avatar
    Pamela Bretscher

    Hi jingchun liu,

    Yes, it is required to let GATK know that you are specifying a genomicsDB rather than a VCF. Please let me know if you have any further questions!

    Kind regards,

    Pamela

    0
    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk