Genome Analysis Toolkit

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

Error on FastaAlternateReferenceMaker process

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    Genevieve Brandt

    Hello JaeJun Lee, could you validate your VCF file Venter.sorted.vcf? You can use ValidateVariants (docs here) following the troubleshooting tutorial here

    The main issue I see is this line, it looks like there is an issue with the file.

    Caused by: java.lang.IllegalArgumentException: Invalid count number, with fixed count the number should be 1 or higher: key=INFO name=TSA type=String desc=Type of sequence alteration. Child of term sequence_alteration as defined by the sequence ontology project. lineType=INFO count=0

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