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

GenotypeGVCFs 'Cannot decompress with GZIP: inflate error: Z_DATA_ERROR'


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    Gökalp Çelik

    Hi Tristan Dennis

    You may want to try running GenotypeGVCFs with latest versions of GATK however this error looks like a corrupt genomicsdb import folder therefore the only option would be to start over to recreate it. 

    Can you tell us how you imported your samples? Did you use incremental updates? If so did you use the consolidate option?

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