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 while running HaplotypeCaller with gatk 4


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    David Benjamin

    Your error message: "A USER ERROR has occurred: t is not a recognized option" is, admittedly, not so clear.  It means that your command has an invalid argument that starts with 't'.  In this case, the culprit is "-targetIntervals," which does not exist in the GATK.  Instead you should use "-intervals" or its short version "-L".

    ## command with argument in question bolded:

    # 2020-04-24 02:55:50 java -Xmx3500m -jar /home/swamy123/softwares/GenomeAnalysisTK/GenomeAnalysisTK.jar HaplotypeCaller -R reference/lambda_virus.fasta -targetIntervals samples/sample3/ -I samples/sample3/reads.sorted.deduped.bam -O samples/sample3/reads.sorted.deduped.indelrealigned.bam

    By the way, the output ends in .bam, which will also result in error.  HaplotypeCaller output files should end in .vcf or .vcf.gz

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