Truvari phab fails to read VCF headers from output file and crashes about truvari HOT 4 CLOSED

The error is sort of pointing to a problem with /home/timdunn/vcfdist/comparison/vcfs/norm/bench.vcf.gz . But I suspect that VCF won't have an issue, either. Instead, I'm thinking there's a problem with something around --bSamples and --cSamples. I can't confirm this without having access to the bench.vcf.gz.

Could you provide the bench.vcf.gz?

Side note: the ability of phab to harmonize two VCFs into one is an almost vestigial function that's largely been superseded by refine. Depending on how this ticket goes I might need remove it.

from truvari.

I'm marking this ticket as abandoned. You can reopen if there are any updates.

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Hi Adam,

So it seems like the intended method for running Truvari at the moment is bench followed by refine, instead of phab followed by bench. Is that correct?

In that case, is there any supported method for refining the counts without modifying any of the variant representations? I'm looking to compare the results of Truvari on a per-variant basis with other tools, and so it seems like the only supported method of doing so is to first call Truvari phab, and then evaluate with multiple tools on that variant callset.

Thanks,
Tim

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Truvari phab was not deprecated. My speculation based on "depending on how this ticket goes" was answered when the issue was fixed.

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