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

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Matteo Costacurta

• April 12, 2023 23:16

Hello GATK team,

I have called variants with Mutect2 and filtered with FilterMutectCalls, generating a final vcf.gz file. When I upload this file in IGV I get this error:

I have tried to view it with bcftools and everything seems fine to me. 

If I decompress with:

bcftools view filename.var.gz > filename.vcf 

It uploads and opens without any issue.

I was wondering if you have an idea of what is happening here.

GATK version used: 4.3.0.0

Cheers

M

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• 

  David Roazen

  • May 12, 2023 19:23

  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. 

  Regards,

  David

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