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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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Added my_variant_info gnomad exome allele frequency fields #124

Closed mandawilson closed 4 years ago

mandawilson commented 4 years ago

If 'my_variant_info' is included in the enrichment fields then the following fields will now be included in the output MAF:

gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF

Which will come from the following Genome Nexus JSON:

"my_variant_info": { "annotation": { "gnomadExome": {"alleleFrequency": { "af": 0, "af_afr": 0, "af_amr": 0, "af_asj": 0, "af_eas": 0, "af_fin": 0, "af_nfe": 0, "af_oth": 0, "af_sas": 0 }}}}

sheridancbio commented 4 years ago

For this PR, whole exome sequencing based allele frequencies were selected for reporting. There were also whole genome sequencing frequencies present, but our choice was made to be most compatible with prior practice, which used gnomAD frequencies generated via VEP runs. According to the following PR in the Ensembl/ensembl-vep repository, the VEP cache is only packaged with whole exome sequencing allele frequencies: https://github.com/Ensembl/ensembl-vep/issues/414