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can't find docs on VCF genotypes format assumptions. Not clear what makes them reset to missing. #3472

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bw2 opened this issue Apr 30, 2018 · 2 comments

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commented Apr 30, 2018

To report a bug, fill in the information below.
For support and feature requests, please use the discussion forum: http://discuss.hail.is/


Hail version: 0.1

What you did:

What went wrong (all error messages here, including the full java stack trace):

The docs under
https://hail.is/docs/stable/hail.HailContext.html?highlight=import_vcf#hail.HailContext.import_vcf
are

If generic equals False (default), Hail makes certain assumptions about the genotype fields, see Representation. On import, Hail filters (sets to no-call) any genotype that violates these assumptions. Hail interprets the format fields: GT, AD, OD, DP, GQ, PL; all others are silently dropped.

but clicking the Representation link does lead to any additional details.

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commented Sep 18, 2018

Given the impending deprecation of 0.1, I'm inclined to say this is a won't-fix. Let me know if you want to go through the code together some day this week, that's the best developer documentation!

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commented Sep 18, 2018

well, most accurate

@tpoterba tpoterba closed this Sep 18, 2018

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