Allow variant annotations to be loaded into genotypes #1838
Comments
|
What are you thinking for resolving this one? Would it be better to roll back before releasing 0.23.0? |
|
I don't think we need to resolve this in 0.23.0 (it can wait for 0.24.0, which will follow fairly shortly thereafter), but it winds up being a pretty straightforward fix that adds a configuration flag. I'll have a patch along shortly. |
|
A configuration flag change should probably go in 0.23.0 then, for better or worse folks stick with release versions. We're still waiting on Hadoop-BAM 7.9.1. |
|
+1 to that; I just wouldn't want it to drag out the 0.23.0 release is all. |
fnothaft
added a commit
to fnothaft/adam
that referenced
this issue
Dec 19, 2017
…igurable. Resolves bigdatagenomics#1838. Modifies the behavior of bigdatagenomics#1771, which disabled populating the `variant.annotation` field in the `Genotype` record. Now, this field is not populated by default. To enable populating it, a user can set the property `org.bdgenomics.adam.converters.VariantContextConverter.NEST_ANN_IN_GENOTYPES` to true.
heuermh
pushed a commit
that referenced
this issue
Dec 20, 2017
…igurable. Resolves #1838. Modifies the behavior of #1771, which disabled populating the `variant.annotation` field in the `Genotype` record. Now, this field is not populated by default. To enable populating it, a user can set the property `org.bdgenomics.adam.converters.VariantContextConverter.NEST_ANN_IN_GENOTYPES` to true.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
In #1771 we stripped variant annotation loading out of genotypes, in favor of keeping the variant annotations stored in the accompanying variant (c.f.,
VariantContext). However, if you're working with single sample data (e.g., gVCFs), having the variant annotation nested under the genotype may be useful.The text was updated successfully, but these errors were encountered: