Gene-level analysis - Githubissues

genepi / nf-gwas

A nextflow pipeline to perform state-of-the-art genome-wide association studies.

https://genepi.github.io/nf-gwas

MIT License

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Gene-level analysis #70

Closed filosi closed 11 months ago

filosi commented 1 year ago

An error is thrown when using plink set files divided by chromosome on gene-level analysis. In particular for: genotype_association=<mydir>/chr*.{bim,bed,fam} Error on REGENIE_STEP2_GENE_TESTS: chr1.bed Not Found

When running with: genotype_association=<mydir>/chr1.{bim,bed,fam}

Everything goes fine.

seppinho commented 11 months ago

This has been fixed by supporting VCF and BGEN for gene-based testing in #92