Strand bias doesn't get exported #1226

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fnothaft opened this Issue Oct 25, 2016 · 3 comments

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fnothaft commented Oct 25, 2016

Similar to #1203, Strand bias does not get properly exported on conversion back to VCF.

@fnothaft fnothaft added the bug label Oct 25, 2016

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heuermh Oct 27, 2016

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Are you referring to VCF INFO reserved key SB?
The corresponding field was intentionally removed from Variant in recent changes.

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heuermh commented Oct 27, 2016

Are you referring to VCF INFO reserved key SB?
The corresponding field was intentionally removed from Variant in recent changes.

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Format key, not info.

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fnothaft commented Oct 27, 2016

Format key, not info.

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I see, so you're saying the fix in #1203 was only on the read side, not the write side.

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heuermh commented Oct 27, 2016

I see, so you're saying the fix in #1203 was only on the read side, not the write side.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 7, 2016

[ADAM-1226] Properly export strand bias components.
Resolves #1226. Adds logic to
`org.bdgenomics.adam.converters.VariantContextConverter` that checks for a
4 element array in the `strandBiasComponents` field. If this is present, this
is exported as the "SB" VCF field.

fnothaft added a commit to fnothaft/adam that referenced this issue Nov 8, 2016

[ADAM-1226] Properly export strand bias components.
Resolves #1226. Adds logic to
`org.bdgenomics.adam.converters.VariantContextConverter` that checks for a
4 element array in the `strandBiasComponents` field. If this is present, this
is exported as the "SB" VCF field.

@heuermh heuermh closed this in 93585e5 Nov 8, 2016

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