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

VariantFiltration Issue


1 comment

  • Avatar
    Megan Shand

    Without seeing the input VCF I can't guarantee that this is the problem, but I suspect that changing "QD < 20" to "QD < 20.0" might help. This is because the error message says:

    java.lang.NumberFormatException: For input string: "33.71"
        at java.lang.NumberFormatException.forInputString(
        at java.lang.Long.parseLong(

    Since the float 33.71 can't be parsed as a long I think that might be the problem. Maybe one of the first variants in your VCF has a QD of 33.71?

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk