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

HaplotypeCaller Follow

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    K S Praharshit Sharma

    Hello, the HaplotypeCaller tool does not seem to work with / without [-T] option, in Latest/ prior Stable versions of GATK. What actually happens is, when GATK is used with [-T] , it reports Error [-T] is an Invalid option. On the other Hand, when HaplotypeCaller is NOT preceded by [-T] qualifier, in this case, the workflow works fine but VCF file is NOT being generated. Kindly resolve this issue at the Earliest !

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