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 loading filtermutectcalls.var.vcf.gz in IGV 2.16.0 - htsjdk.samtools.util.RuntimeIOException [file] has invalid uncompressedLength


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    David Roazen

    Hi Matteo Costacurta,

    Can you please check your .vcf.gz file with the GATK tool PrintBGZFBlockInformation? This tool will check the compressed blocks within the file to see if any are corrupt or contain incorrect metadata. 



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