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

Genotype concordance


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    Genevieve Brandt (she/her)

    Hi Priya,

    This indicates that your VCF files do not have matching sequence dictionaries. The sequence dictionary in a VCF header are the lines with the contig names and lengths, corresponding to the BAM file. Your error message indicates that your VCF files were generated from different reference versions or there are issues with the sequence dictionaries.

    You can examine these sequence dictionary lines in the header to find out what is your mismatch.



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