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Where can I find "Phred-scaled quality score" (QUAL)? #1506

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majkiw opened this Issue Apr 27, 2017 · 2 comments

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@majkiw
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majkiw commented Apr 27, 2017

Hey,
Following instructions in https://github.com/bigdatagenomics/adam/wiki/FAQ-(Frequently-Asked-Questions) and http://bdgenomics.org/mail/ I created a question in Google Groups https://groups.google.com/forum/#!topic/adam-developers/WNu5a8wIwz8
Since I don't think anyone looks there anymore it I will ask it here again.

When reading VCF I cannot find "Phred-scaled quality score" (QUAL) and even htsjdkVC.getPhredScaledQual doesn't seem to be accessed anywhere.
I also don't see the values when printing the whole Genotype object.
Is the QUAL field omitted on purpose or am I missing something obvious?

Thank you,
Michał Wysocki

@majkiw majkiw changed the title from Where can I find "Phred-scaled quality score" (QUAL) to Where can I find "Phred-scaled quality score" (QUAL)? Apr 27, 2017

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heuermh Apr 27, 2017

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Sorry for not seeing your post on the mailing list!

In the VCF specification, QUAL is defined

6. QUAL - quality: Phred-scaled quality score for the assertion made
in ALT. i.e. −10log10 prob(call in ALT is wrong). If ALT is ‘.’ (no variant) then
this is −10log10 prob(variant), and if ALT is not ‘.’ this is −10log10 prob(no variant).
If unknown, the missing value should be specified. (Float)

We use a split-allelic model, where each ALT at a site is a separate Variant. There is no way to distribute this per-site quality score over all the separate variants so we have to drop it.

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heuermh commented Apr 27, 2017

Sorry for not seeing your post on the mailing list!

In the VCF specification, QUAL is defined

6. QUAL - quality: Phred-scaled quality score for the assertion made
in ALT. i.e. −10log10 prob(call in ALT is wrong). If ALT is ‘.’ (no variant) then
this is −10log10 prob(variant), and if ALT is not ‘.’ this is −10log10 prob(no variant).
If unknown, the missing value should be specified. (Float)

We use a split-allelic model, where each ALT at a site is a separate Variant. There is no way to distribute this per-site quality score over all the separate variants so we have to drop it.

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majkiw Apr 28, 2017

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Thank you for the quick response.
I read the definition before but I didn't realize split-allelic approach breaks it.

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majkiw commented Apr 28, 2017

Thank you for the quick response.
I read the definition before but I didn't realize split-allelic approach breaks it.

@majkiw majkiw closed this Apr 28, 2017

@heuermh heuermh modified the milestone: 0.23.0 Jul 22, 2017

@heuermh heuermh added this to Completed in Release 0.23.0 Jan 4, 2018

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