tensorqtl_trans
tensorQTL trans mode output format
Overview
| Field |
Value |
| Format key |
tensorqtl_trans |
| Spec file |
formats/tensorqtl_trans.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 |
|
| Raw header |
Canonical |
af |
EAF |
b |
BETA |
b_se |
SE |
phenotype_id |
TRAIT |
pval |
P |
r2 |
R2 |
variant_id |
SNPID |
| ## Header descriptions |
|
| Column |
Description |
af |
In-sample ALT allele frequency of the variant |
b |
Regression slope |
b_se |
Standard error of the regression slope |
phenotype_id |
Phenotype ID |
pval |
Nominal p-value of the association between the phenotype and variant |
r2 |
Squared residual genotype-phenotype correlation (only generated if map_trans(..., return_r2=True)) |
variant_id |
Variant ID |
| ## Coverage |
|
5/9 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 |
yes |
BETA |
OR, HR, Z |
| Uncertainty |
yes |
SE |
— |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
no |
— |
N, N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
no |
— |
INFO |
| ## See also |
|
|
|