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SelectVariants no suitable codecs found

atariatari SwitzerlandMember

Hi, I am trying to run SelectVariants (gatk on the vcf output of FilterMutectCalls.
I get the following error:

org.broadinstitute.hellbender.exceptions.UserException$NoSuitableCodecs: Cannot read file:///hpcnfs/scratch/CRU/afranceschini/htsflow/provaB2.vcf.gz because no suitable codecs found
at org.broadinstitute.hellbender.engine.FeatureManager.getCodecForFile(FeatureManager.java:468)

What could it be ? Thx a lot


  • atariatari SwitzerlandMember

    Sorry for the previous question. Please discard it.
    It was giving me that error simply because I had accidentally removed the CHROM header in the input vcf.

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