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Erik Fasterius

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Latest activity by Erik Fasterius
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    Erik Fasterius commented,

    Ah, that was indeed the problem! I was not giving it the tranches file, but rather the recal file once again. Definitely a user error here, totally my fault, but I wonder why the error message is s...

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    Erik Fasterius commented,

    Just did, for both recal files (which indeed gives .idx files rather than .tbi), but the exact same error remains. I have also tried re-running the the entire process, but the results are the same :-(

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    Erik Fasterius commented,

    I've now removed the index file (which was a tabix file, .tbi, not .idx) and run the IndexFeatureFile, which also created a tabix file rather than .idx. The command ran successfully: $ gatk IndexFe...

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    Erik Fasterius commented,

    Hi, Bhanu! I already tried to re-create the recal file, and still get the same error when running ApplyVQSR. Here is parts of the recal header (shortened for brevity with its tranches and contigs) ...

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    Erik Fasterius created a post,

    Recal file with malformed header

    Hi, I'm trying to run VQSR as per the documentation, and I've successfully run the variant recalibration step for both indels and SNVs, but I get an error when trying to apply these recalibrations:...