Mutect2 --alleles param GATK_4.1.7.0

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registered_user

• June 26, 2020 14:54
• Edited

What's going on with the --alleles param for Mutect2? It will not accept a .vcf, .vcf.gz, .list or .intervals file (<chr>:<coordinate>). I have an index for the .vcf.gz file, .vcf.gz.tbi. I am getting:

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A USER ERROR has occurred: Cannot read file:///data/test_alleles.vcf.gz because no suitable codecs found

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Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.1.7.0-local.jar

A more helpful error msg would be nice and the docs should say what file formats are accepted, rather than just "FeatureInput[VariantContext]".

 

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  registered_user

  • June 26, 2020 20:18

  Having "##fileformat=VCFv4.2" at the beginning of the --alleles .vcf.gz file seems to have done the trick.

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  Bhanu Gandham

  • June 28, 2020 01:30

  Thanks for the update registered_user. This will help other users.

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