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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

GATK VariantFiltration Error

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    Pamela Bretscher

    Hi Reza,

    I found several previous forum posts with the same error while running VariantFiltration which might have some helpful troubleshooting advice for you:

    https://gatk.broadinstitute.org/hc/en-us/community/posts/360072140012-Variant-Filtration-error-Number-format-exception-

    https://gatk.broadinstitute.org/hc/en-us/community/posts/360072157591-NumberFormatException-Error-in-VariantFiltration

    It looks like it may be an issue with the filters running into a string in your files. Could you take a look at these previous suggestions and let me know if they are helpful?

    Kind regards,

    Pamela

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    Reza

    Sorry for the delay; Thanks Pamela for your answer but I do not find any solution to my problem. I ran ValidateVariants and everything is OK. I decided to use bcftools for filtration VCF file. Do you recommend using another program to filter the VCF file outputted from GATK? Because otherwise my work will be half done.

    input string error is a java issue or GATK?

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    Pamela Bretscher

    Hi Reza,

    Thank you for your response and for running ValidateVariants. The input string error is a java issue with the JEXL expression rather than a GATK issue with your files. I believe this is why your ValidateVariants output looks good. I think your initial problem is coming from an incompatibility between the expressions you specify for filtration (i.e. MQ<40) and the string the tool is running into (10.90). This is because you are specifying an integer value but the tool is running into a non-integer value, causing the error. This article explains this more. 

    Was bcftools successful for you in filtering the VCF? I would recommend using VariantFiltration to try to avoid incompatibilities between GATK and other tools. I believe you can try adding '.0' for the float values to avoid the error with the '10.90' input string. Please let me know if you have any other questions or concerns.

    Kind regards,

    Pamela

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