feat: refactoring vep annotation step #67
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DSuveges
reviewed
Nov 5, 2024
| @@ -205,134 +248,3 @@ def _vep_command(self) -> list[str]: | |||
| --plugin AlphaMissense,file={self.pm.cache_dir}/AlphaMissense_hg38.tsv.gz,transcript_match=1 \ | |||
| --plugin CADD,snv={self.pm.cache_dir}/CADD_GRCh38_whole_genome_SNVs.tsv.gz", | |||
| ] | |||
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| class ConvertVariantsToVcfOperator(BaseOperator): | |||
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As I understand,this is no longer needed, because this functionality is done by a separate step, right?
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This is no longer needed, as it is a part of the variant_to_vcf step -> https://github.com/opentargets/gentropy/blob/4d8e7c42e8e94473495d12d50efb7d7942afbe73/src/gentropy/variant_index.py#L114
DSuveges
approved these changes
Nov 5, 2024
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Context
This PR is a part of effort to reduce the complexity of genetics_etl dag. Due to the fact that we want to submerge the genetics_etl to the platform etl dag, we need to simplify the VariantAnnotation task group.
Implementations
This PR changes the logic of
variant_annotationnode in the genetics etl dag.variant_to_vcfdag node implementation:Node was previously running as a google batch job with 4
variant_to_vcfgentropy steps (one per each datasource* uniprot
* eva
* credible sets
* pharmgkb)
that was followed by
local(run with python operator -ConvertVariantsToVcfOperator) partitioning of the vcf based data sources.With refactoring of
variant_to_vcfstep implemented in refactor(convert to vcf): allow multiple input sources gentropy#891 the step can now take n datasources that are running in sequence and produce a single partitioned dataset. This allows for the:ConvertVariantsToVcfOperatoris no longer there#in the column name without quoting the column name - issue comes whenvariant_to_vcfwants to save the#CHROMcolumn as"#CHROM"creating the following issue in VEP:Note
This PR requires the opentargets/gentropy#896 to be merged, as the
#CHROMissue was resolved by dynamically change theCHROMto#CHROM, so thevariant_to_vcfstep should drop the hash.