Post by joelle on Jul 12, 2022 13:47:24 GMT
Hello!
When running sBLUP I encounter the following error:
Accepted options:
--bfile xx
--exclude exclude.snps
--cojo-file yy.ma
--cojo-sblup 6.51215e+06
--cojo-wind 1000
--thread-num 20
--maf 0.01
--out zz
Reading PLINK FAM file from [xx.fam].
8343 individuals to be included from [xx.fam].
Reading PLINK BIM file from [xx.bim].
1135234 SNPs to be included from [xx.bim].
Reading a list of SNPs from [exclude.snps].
12 SNPs are excluded from [exclude.snps] and there are 1135222 SNPs remaining.
Reading PLINK BED file from [xx.bed] in SNP-major format ...
Genotype data for 8343 individuals and 1135222 SNPs to be included from [xx.bed].
Calculating allele frequencies ...
Filtering SNPs with MAF > 0.01 ...
After filtering SNPs with MAF > 0.01, there are 1135222 SNPs (0 SNPs with MAF < 0.01).
Reading GWAS summary-level statistics from [yy.ma] ...
GWAS summary statistics of 1211232 SNPs read from [yy.ma].
Phenotypic variance estimated from summary statistics of all 1211232 SNPs: 5.45094 (variance of logit for case-control studies).
Matching the GWAS meta-analysis results to the genotype data ...
Warning: can't match the reference alleles or of 12 SNPs to those in the genotype data. These SNPs have been saved in [zz.badsnps].
75 SNP(s) have large difference of allele frequency among the GWAS summary data and the reference sample. These SNPs have been saved in [zz.freq.badsnps].
1134745 SNPs are matched to the genotype data.
Calculating the variance of SNP genotypes ...
Performing joint analysis on all the 1134745 SNPs ...
(Assuming complete linkage equilibrium between SNPs which are more than 1Mb away from each other)
Error: there are 5 SNPs with MAF=0.
An error occurs, please check the options or data
This happens even though I filtered both input files at MAF 0.01, and manually removed SNPs with missing AF after running plink --freq. I also tried running it with '--exclude zz.freq.badsnps' which is created in this step, all to no avail. Does anyone know what could be the issue?
When running sBLUP I encounter the following error:
Accepted options:
--bfile xx
--exclude exclude.snps
--cojo-file yy.ma
--cojo-sblup 6.51215e+06
--cojo-wind 1000
--thread-num 20
--maf 0.01
--out zz
Reading PLINK FAM file from [xx.fam].
8343 individuals to be included from [xx.fam].
Reading PLINK BIM file from [xx.bim].
1135234 SNPs to be included from [xx.bim].
Reading a list of SNPs from [exclude.snps].
12 SNPs are excluded from [exclude.snps] and there are 1135222 SNPs remaining.
Reading PLINK BED file from [xx.bed] in SNP-major format ...
Genotype data for 8343 individuals and 1135222 SNPs to be included from [xx.bed].
Calculating allele frequencies ...
Filtering SNPs with MAF > 0.01 ...
After filtering SNPs with MAF > 0.01, there are 1135222 SNPs (0 SNPs with MAF < 0.01).
Reading GWAS summary-level statistics from [yy.ma] ...
GWAS summary statistics of 1211232 SNPs read from [yy.ma].
Phenotypic variance estimated from summary statistics of all 1211232 SNPs: 5.45094 (variance of logit for case-control studies).
Matching the GWAS meta-analysis results to the genotype data ...
Warning: can't match the reference alleles or of 12 SNPs to those in the genotype data. These SNPs have been saved in [zz.badsnps].
75 SNP(s) have large difference of allele frequency among the GWAS summary data and the reference sample. These SNPs have been saved in [zz.freq.badsnps].
1134745 SNPs are matched to the genotype data.
Calculating the variance of SNP genotypes ...
Performing joint analysis on all the 1134745 SNPs ...
(Assuming complete linkage equilibrium between SNPs which are more than 1Mb away from each other)
Error: there are 5 SNPs with MAF=0.
An error occurs, please check the options or data
This happens even though I filtered both input files at MAF 0.01, and manually removed SNPs with missing AF after running plink --freq. I also tried running it with '--exclude zz.freq.badsnps' which is created in this step, all to no avail. Does anyone know what could be the issue?