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Support INFO fields set to missing #1898

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fnothaft opened this issue Feb 1, 2018 · 1 comment
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Support INFO fields set to missing #1898

fnothaft opened this issue Feb 1, 2018 · 1 comment
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@fnothaft
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@fnothaft fnothaft commented Feb 1, 2018

While the best practice for missing VCF INFO fields is to omit them from the INFO column for the variant with the missing field, the VCF spec is actually quite loose about this being the correct way to do things:

The exact format of each INFO sub-field should be specified in the meta-information (as described above). Example for an INFO field: DP=154;MQ=52;H2. Keys without corresponding values are allowed in order to indicate group membership (e.g. H2 indicates the SNP is found in HapMap 2). It is not necessary to list all the properties that a site does NOT have, by e.g. H2=0. See below for additional reserved INFO sub-fields used to encode structural variants.

We throw if we see an INFO field with a missing value ..

@fnothaft fnothaft added the bug label Feb 1, 2018
@fnothaft fnothaft added this to the 0.24.0 milestone Feb 1, 2018
@fnothaft fnothaft self-assigned this Feb 1, 2018
@heuermh
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@heuermh heuermh commented Feb 1, 2018

By best practice, are you taking only about Number=0,Type=Flag?

I suppose Number=. may also allow missing values (SVLEN=.) or missing keys (no SVLEN) but I'm not sure about the others Number=1,n,A,R,G.

##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in
length between REF and ALT alleles">
fnothaft pushed a commit to fnothaft/adam that referenced this issue Feb 2, 2018
Resolves bigdatagenomics#1898. Also fixes an issue with converting negative phred values.
@heuermh heuermh closed this in #1899 Feb 2, 2018
heuermh added a commit that referenced this issue Feb 2, 2018
Resolves #1898. Also fixes an issue with converting negative phred values.
@heuermh heuermh added this to Completed in Release 0.24.0 Feb 10, 2018
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