Post by Anna Docherty on Nov 5, 2019 20:30:07 GMT
Hello--why is mtCOJO generating h2s of >1.0 for everything I put in? Regardless of p-value threshold? Some sample output here with MDD and SZ at p = 10-6:
Accepted options:
--bfile /mnt/d/UoU/GenotypeData/1000G/EUR/EUR
--mtcojo-file sums/summary_4_10B.txt
--ref-ld-chr /mnt/d/UoU/tools/gcta/eur_w_ld_chr_my/
--w-ld-chr /mnt/d/UoU/tools/gcta/eur_w_ld_chr_my/
--out outE3/test410B_1e-6
--gwas-thresh 1e-06
Reading PLINK FAM file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.fam].
503 individuals to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.fam].
Reading PLINK BIM file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bim].
78089847 SNPs to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bim].
Reading GWAS summary data from [sums/summary_4_10B.txt] ...
7760164 SNPs in common between the target trait and the covariate trait(s).
Filtering out SNPs with multiple alleles or missing value ...
7760164 SNPs are retained after filtering.
There are 14023 genome-wide significant SNPs with p < 1.0e-06.
Reading PLINK BED file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bed] in SNP-major format ...
Genotype data for 503 individuals and 14023 SNPs to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bed].
Calculating allele frequencies ...
Checking the difference in allele frequency between the GWAS summary datasets and the LD reference sample...
33682 SNP(s) have large difference of allele frequency among the GWAS summary data and the reference sample. These SNPs have been saved in [outE3/test410B_1e-6.freq.badsnps].
Univariate LD score regression analysis to estimate SNP-based heritability ...
MDD: 1.001795 0.059940
Schizophrenia: 1.053510 0.237378
Bivariate LD score regression analysis to estimate genetic correlation between each pair of traits ...
Intercept:
1.00179 0.0425597
0.0425597 1.05351
rg:
0.0599397 0.328177
0.328177 0.237378
The LD score regression analyses completed.
GSMR analysis for covariate #1 (Schizophrenia) ...
223 index SNPs are obtained from the clumping analysis with p < 1.0e-06 and LD r2 < 0.05.
15 pleiotropic SNPs are filtered by HEIDI-outlier analysis.
208 index SNPs are retained after HEIDI-outlier analysis.
bxy 0.065951 0.004966
GSMR analysis for covariate #1 (Schizophrenia) completed.
The pleiotropic SNPs filtered by HEIDI-outlier analysis have been saved in [outE3/test410B_1e-6.pleio_snps].
mtCOJO analysis ...
There are 7726482 SNPs in common between the target trait and all the covariate trait(s).
Saving the mtCOJO analysis results of 7726482 remaining SNPs to [outE3/test410B_1e-6.mtcojo.cma] ...
mtCOJO analysis completed.
Accepted options:
--bfile /mnt/d/UoU/GenotypeData/1000G/EUR/EUR
--mtcojo-file sums/summary_4_10B.txt
--ref-ld-chr /mnt/d/UoU/tools/gcta/eur_w_ld_chr_my/
--w-ld-chr /mnt/d/UoU/tools/gcta/eur_w_ld_chr_my/
--out outE3/test410B_1e-6
--gwas-thresh 1e-06
Reading PLINK FAM file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.fam].
503 individuals to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.fam].
Reading PLINK BIM file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bim].
78089847 SNPs to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bim].
Reading GWAS summary data from [sums/summary_4_10B.txt] ...
7760164 SNPs in common between the target trait and the covariate trait(s).
Filtering out SNPs with multiple alleles or missing value ...
7760164 SNPs are retained after filtering.
There are 14023 genome-wide significant SNPs with p < 1.0e-06.
Reading PLINK BED file from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bed] in SNP-major format ...
Genotype data for 503 individuals and 14023 SNPs to be included from [/mnt/d/UoU/GenotypeData/1000G/EUR/EUR.bed].
Calculating allele frequencies ...
Checking the difference in allele frequency between the GWAS summary datasets and the LD reference sample...
33682 SNP(s) have large difference of allele frequency among the GWAS summary data and the reference sample. These SNPs have been saved in [outE3/test410B_1e-6.freq.badsnps].
Univariate LD score regression analysis to estimate SNP-based heritability ...
MDD: 1.001795 0.059940
Schizophrenia: 1.053510 0.237378
Bivariate LD score regression analysis to estimate genetic correlation between each pair of traits ...
Intercept:
1.00179 0.0425597
0.0425597 1.05351
rg:
0.0599397 0.328177
0.328177 0.237378
The LD score regression analyses completed.
GSMR analysis for covariate #1 (Schizophrenia) ...
223 index SNPs are obtained from the clumping analysis with p < 1.0e-06 and LD r2 < 0.05.
15 pleiotropic SNPs are filtered by HEIDI-outlier analysis.
208 index SNPs are retained after HEIDI-outlier analysis.
bxy 0.065951 0.004966
GSMR analysis for covariate #1 (Schizophrenia) completed.
The pleiotropic SNPs filtered by HEIDI-outlier analysis have been saved in [outE3/test410B_1e-6.pleio_snps].
mtCOJO analysis ...
There are 7726482 SNPs in common between the target trait and all the covariate trait(s).
Saving the mtCOJO analysis results of 7726482 remaining SNPs to [outE3/test410B_1e-6.mtcojo.cma] ...
mtCOJO analysis completed.