ldsc
Overview
| Field |
Value |
| Format key |
ldsc |
| Spec file |
formats/ldsc.json |
| Cite name |
LDSC |
| Version |
20150306 |
| Source |
https://github.com/bulik/ldsc/wiki/Summary-Statistics-File-Format |
| Source (2) |
https://github.com/bulik/ldsc/blob/master/munge_sumstats.py |
| GitHub |
https://github.com/bulik/ldsc |
| Citation |
Bulik-Sullivan, B. K., Loh, P. R., Finucane, H. K., Ripke, S., Yang, J., Patterson, N., ... & Neale, B. M. (2015). LD Score regression distinguishes confounding from polygenicity in genome-wide association studies. Nature genetics, 47(3), 291-295. |
| ## Column mapping |
|
| Raw header |
Canonical |
Canonical (secondary) |
A1 |
EA |
— |
A2 |
NEA |
— |
Beta |
BETA |
— |
CHR |
CHR |
— |
Frq |
EAF |
— |
INFO |
INFO |
— |
N |
N |
— |
OR |
OR |
— |
P |
P |
— |
POS |
POS |
— |
SNP |
rsID |
SNPID |
Z |
Z |
— |
| ## Coverage |
|
|
8/9 tier groups satisfied.
| Tier |
Status |
Matched |
Missing |
| Variant ID |
yes |
SNPID, rsID |
— |
| Genomic location |
yes |
CHR, POS |
— |
| Effect / other allele |
yes |
EA, NEA |
— |
| Effect size |
yes |
BETA, OR, Z |
HR |
| Uncertainty |
no |
— |
SE |
| P-value |
yes |
P |
MLOG10P |
| Sample size |
yes |
N |
N_CASE |
| Allele frequency |
yes |
EAF |
MAF, NEAF |
| Imputation / QC |
yes |
INFO |
— |
| ## See also |
|
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