ldsc_preprocess inputs

[rbutleriii]

Hello, I used SAIGE to generate my individual level sumstats, and it returns the BETA and SE for each phenotype. And a Tstat not a Z. Full stats:

CHR: chromosome
POS: genome position 
SNPID: variant ID
Allele1: allele 1
Allele2: allele 2
AC_Allele2: allele count of allele 2
AF_Allele2: allele frequency of allele 2
imputationInfo: imputation info. If not in dosage/genotype input file, will output 1
N: sample size
BETA: effect size of allele 2
SE: standard error of BETA
Tstat: score statistic of allele 2
p.value: p value (with SPA applied for binary traits)
p.value.NA: p value when SPA is not applied (only for binary traits)
Is.SPA.converge: whether SPA is converged or not (only for binary traits)
varT: estimated variance of score statistic with sample relatedness incorporated
varTstar: variance of score statistic without sample relatedness incorporated
AF.Cases: allele frequency of allele 2 in cases (only for binary traits and if --IsOutputAFinCaseCtrl=TRUE)
AF.Controls: allele frequency of allele 2 in controls (only for binary traits and if --IsOutputAFinCaseCtrl=TRUE)
Tstat_cond, p.value_cond, varT_cond, BETA_cond, SE_cond: summary stats for conditional analysis

Is there a way to input these directly into ldsc_precprocess.py rather than trying to compute a Z (probably with munge_sumstats.py)? Can I calculate the first table directly from these and use the genetic covariance and environmental correlation matrices from ldsc_preprocess.py?

[cuelee]

Thank you for your inquiry. And sorry for the late reply.

Unfortunately, the current code does not support SAIGE. The PLEIO code can use the input of LDSC by default.