Processes pQTL summary statistics into Hail Tables with Ensembl ID mapping.
npx skills add https://github.com/bigbio/hvantk --skill pqtl
Please help me install this Agent Skill. Skill: pqtl Source: https://github.com/bigbio/hvantk/tree/main/hvantk/skills/pqtl Command: npx skills add https://github.com/bigbio/hvantk --skill pqtl
This skill addresses the challenge of integrating protein quantitative trait loci (pQTL) data with genetic variant annotations, enabling researchers to link genetic variants to protein abundance levels across diverse tissues.
Use the pqtl skill to process the Fang et al. pQTL dataset by running the hvantk reprocess command with the required HGNC lookup table path.
High-intent search queries and answers about installing and using this skill.
To integrate pQTL summary statistics into Hail Tables, you can process and parse GTEx-derived pQTL allpairs data. This ingests protein quantitative trait loci metrics into Hail to enable downstream multiomics variant analysis.
Mapping gene symbols to Ensembl IDs requires a valid HGNC lookup table to ensure data consistency. This standardization step ensures compatibility when performing downstream cascade joins with existing eQTL datasets.
Yes, Hail is a required dependency for processing GTEx pQTL allpairs data. You must run the processing commands within a Hail environment to successfully build standardized Hail Tables.
Yes, integrating pQTL data links genetic variants to protein abundance levels across diverse tissues. It processes Fang et al. (2025) GTEx tissue data to improve the functional interpretation of genetic variants.
An HGNC lookup table is required to ensure data consistency across heterogeneous omics sources. It facilitates the accurate mapping of gene symbols to Ensembl gene IDs before joining with eQTL datasets.
The main limitation is ensuring data consistency across heterogeneous omics sources. You must supply a valid HGNC lookup table and use Hail to properly standardize the pQTL metrics for functional interpretation.
bigbioMap legacy gene symbols and aliases to canonical HGNC identifiers.
bigbioStandardize GTEx cis-eQTL summary statistics into unified Hail Tables.
bigbioPredict functional effects of genetic variants using the AlphaGenome API.
ammawlaRetrieve GTEx median TPM values to validate ENCODE regulatory findings.
