Beomjin Jang
Towfique Raj Lab
Mount Sinai, New York
2025
Snakemake pipeline for running genome-wide SAIGE-QTL with common variants.
The inputs required by the user are a sampleKey matching RNA samples to DNA samples, a bfile containing the genotype information.
The sample key must have two columns named participant_id listing the names of the genotype IDs and sample_id listing the name of the phenotype sample IDs.
The genotypes must be in bfile format with all chromsomes in a single file with prefix 'chr'.
The phenoMeta must be a tab-separated table with feature information including chr, start and end.(chr, start, end, feature)
The Phenotype can be either space or tab-delimited with a header. It is required that the file contains one column for sample IDs and one more columns for the phenotype. It may contain columns for covariates.
The covarColList should be covariate columns in Phenotype.
The sampleCovarColList should be covariate columns for samples in Phenotype, which have the same values for all cells from the same individual.
The sampleIDColinphenoFile should be genotype IDs column in Phenotype.
Please take a look at the format details on SAIGE-QTL-doc.
- threads
Number of threads to use for runSAIGEQTL rule mclapply parallelization