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Feature request for VariantsToTable: option to preserve numeric genotypes #8160

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bensprung opened this issue Jan 12, 2023 · 4 comments · May be fixed by #8219
Open

Feature request for VariantsToTable: option to preserve numeric genotypes #8160

bensprung opened this issue Jan 12, 2023 · 4 comments · May be fixed by #8219
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@lbergelson

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@bensprung
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bensprung commented Jan 12, 2023 •
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Following the discussion here, I'd like to request a feature for VariantsToTable. Currently, when genotypes are specified via -GF GT, the numeric genotypes (e.g. 0/1) from the input VCF are replaced in the output TSV by the actual alleles (e.g. CTACCCT/AACCCA). I can see why that behavior would be desirable sometimes, but in cases where there are a lot of long variants and a lot of samples, this makes the resulting TSV file quite a bit more hefty than it needs to be (since that info is already in the REF and ALT fields). Therefore I think an option to output the original numeric genotypes from the VCF would be useful. Thanks!
@lbergelson
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@bensprung So I thought this would be a trivial change. It turns out that encoding the Genotype as something like 1/1 is done way down in the depths of the VCF encoder and isn't exposed in an accessible way. It's going to need a (hopefully simple) change to the underlying htsjdk library to expose that machinery. It shouldn't be hard, it just means it will take a bit longer to get to than I expected.

@bensprung
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Well, no worries, thanks so much for working on it!

lbergelson added a commit to samtools/htsjdk that referenced this issue Jan 27, 2023
@lbergelson
Expose the ability to encode a Genotoype into a GT field
6f5230f 
* Expose two public methods in VCFEncoder writeGtField and encodeGtField
* Supports broadinstitute/gatk#8160 but seems like a useful thing to be able to do in general
* minor breaking change in VCFEncoder, made methods formatVCFField and buildAlleleStrings static
  It is unlikely anyone overrides either of these methods so it should not be a problem.
@lbergelson lbergelson mentioned this issue Jan 27, 2023
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@droazen
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droazen commented Jan 30, 2023

Blocked on samtools/htsjdk#1648

lbergelson added a commit to samtools/htsjdk that referenced this issue Jan 30, 2023
@lbergelson
Expose the ability to encode a Genotoype into a GT field
900cd5c 
* Expose two public methods in VCFEncoder writeGtField and encodeGtField
* Supports broadinstitute/gatk#8160 but seems like a useful thing to be able to do in general
* minor breaking change in VCFEncoder, made methods formatVCFField and buildAlleleStrings static
  It is unlikely anyone overrides either of these methods so it should not be a problem.
lbergelson added a commit to samtools/htsjdk that referenced this issue Jan 31, 2023
@lbergelson
Expose the ability to encode a Genotoype into a GT field (#1648)
8108d56 
* Expose the ability to encode a Genotoype into a GT field by exposing
 two public methods in VCFEncoder: writeGtField and encodeGtField
* Supports broadinstitute/gatk#8160 but seems like a useful thing to be able to do in general
* minor breaking change in VCFEncoder, made methods formatVCFField and buildAlleleStrings static
  It is unlikely anyone overrides either of these methods so it should not be a problem.
@lbergelson
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The necesssary change went into htsjdk so we can do this now whenever we pick up a new release of htsjdk.

@lbergelson lbergelson linked a pull request Feb 22, 2023 that will close this issue
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lbergelson added a commit that referenced this issue Feb 22, 2023
@lbergelson
Add a --numeric-gt option to VariantsToTable
aa08065 
* add an new option to VariantsToTable to allow output VCF style numeric GT fields
previously it always output the actual bases of the Allele in the GT spot
* resolves #8160
* updates htsjdk to 3.0.5
lbergelson added a commit that referenced this issue Aug 16, 2024
@lbergelson
Add a --numeric-gt option to VariantsToTable
20e34e8 
* add an new option to VariantsToTable to allow output VCF style numeric GT fields
previously it always output the actual bases of the Allele in the GT spot
* resolves #8160
* updates htsjdk to 3.0.5
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Add a --numeric-gt option to VariantsToTable broadinstitute/gatk
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@droazen @lbergelson @bensprung