tensorqtl_cis_nominal_interaction¶

tensorQTL cis-nominal mode with interaction term output format

Overview¶

Field	Value
Format key	`tensorqtl_cis_nominal_interaction`
Spec file	`formats/tensorqtl_cis_nominal_interaction.json`
Cite name	tensorQTL
Version	20220726
Source	https://raw.githubusercontent.com/broadinstitute/tensorqtl/refs/heads/master/docs/outputs.md
GitHub	https://github.com/broadinstitute/tensorqtl
Citation	Taylor-Weiner, A., Aguet, F., Jones, M., Zaitlen, N., Daly, M., & Ardlie, K. (2019). Scaling computational genomics to millions of individuals with GPUs. Genome Biology, 20, 183.
## Column mapping

Column	Description
`af`	In-sample ALT allele frequency of the variant
`b_g`	Slope of the genotype term
`b_g_se`	Standard error of b_g
`b_gi`	Slope of the interaction term
`b_gi_se`	Standard error of b_gi
`b_i`	Slope of the interaction variable
`b_i_se`	Standard error of b_i
`end_distance`	Distance between the variant and phenotype end position (only present if different from start position)
`ma_count`	Number of minor alleles
`ma_samples`	Number of samples carrying at least one minor allele
`phenotype_id`	Phenotype ID
`pval_adj_bh`	Benjamini-Hochberg adjusted pval_emt
`pval_emt`	Bonferroni-adjusted pval_gi (i.e., multiplied by M_eff)
`pval_g`	Nominal p-value of the genotype term
`pval_gi`	Nominal p-value of the interaction term
`pval_i`	Nominal p-value of the interaction variable
`start_distance`	Distance between the variant and phenotype start position (e.g., TSS)
`tests_emt`	Effective number of independent variants (M_eff) estimated by eigenMT
`variant_id`	Variant ID
## Coverage

2/9 tier groups satisfied.

Tier	Status	Matched	Missing
Variant ID	yes	SNPID	rsID
Genomic location	no	—	CHR, POS
Effect / other allele	no	—	EA, NEA
Effect size	no	—	BETA, OR, HR, Z
Uncertainty	no	—	SE
P-value	no	—	P, MLOG10P
Sample size	no	—	N, N_CASE
Allele frequency	yes	EAF	MAF, NEAF
Imputation / QC	no	—	INFO
## See also