IVG error htsjdk.tribble.TribbleException$InternalCodecException

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allasmo

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Jul 13, 2016, 1:38:54 PM7/13/16

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Dear All,

We experience the following error when trying to load vcf file and focus on a particular mutation:

Error loading features for interval: chr7:6037036-6037077 htsjdk.tribble.TribbleException$InternalCodecException: The allele with index 2 is not defined in the REF/ALT columns in the record, for input source:

//CLNPROD/AdvSeq/Projects/WB_v1/CLHCTHLAFXX_WB_v1_16_0624_12/BamFiles/G-WBv116-230_S14/CLHCTHLAFXX_G-WBv116-230_S14.vcf

Please find the fragment of vcf file and the image of the browser attached and advice how to resolve this situation.

Many thanks!

Alla Smolgovsky

Quest Diagnostics

IGV_image_4_broad.jpg

vcf_fragment_4Broad.txt

Jim Robinson

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Jul 13, 2016, 1:45:49 PM7/13/16

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Hi,

I assume you are using the latest IGV since you didn't specify. The error is indicating an incorrectly formatted VCF file. This is not the best forum to resolve VCF issues, I suggest you post on either the GATK forum, http://gatkforums.broadinstitute.org/gatk, or the forum for whatever tool produced the VCF.

Jim

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