Post by bn on Aug 26, 2014 12:10:11 GMT
Hello,
I have with me only the summary stats data and need to perform conditional analysis on a given set of index SNP list and for the reference file, I am using one of the many participating cohorts in the same meta-analysis
However, when I run the analysis with the following command
I get an Error saying
This cannot be, majority of the SNPs present in the summarystats are surely present in the reference file with the same genotypes.
I have also attached the log file:
Can you help ?
Thank you.
I have with me only the summary stats data and need to perform conditional analysis on a given set of index SNP list and for the reference file, I am using one of the many participating cohorts in the same meta-analysis
However, when I run the analysis with the following command
./gcta64 --bfile CEU --cojo-file summarystats.ma --cojo-cond cond.snplist --out test
I get an Error saying
Error all the SNPs in the GWAS meta-analysis results can't be found in the genotype data
This cannot be, majority of the SNPs present in the summarystats are surely present in the reference file with the same genotypes.
I have also attached the log file:
*******************************************************************
* Genome-wide Complex Trait Analysis (GCTA)
* version 1.24.4
* (C) 2010-2013 Jian Yang, Hong Lee, Michael Goddard and Peter Visscher
* The University of Queensland
* MIT License
*******************************************************************
Analysis started: Tue Aug 26 13:15:45 2014
Options:
--bfile CEU
--cojo-file summarystats.ma
--cojo-cond cond.snplist
--out test
Reading PLINK FAM file from [CEU.fam].
11789 individuals to be included from [CEU.fam].
Reading PLINK BIM file from [CEU.bim].
529205 SNPs to be included from [CEU.bim].
Reading PLINK BED file from [CEU.bed] in SNP-major format ...
Genotype data for 11789 individuals and 529205 SNPs to be included from [CEU.bed].
Reading GWAS summary-level statistics from [summarystats.ma] ...
GWAS summary statistics of 8131642 SNPs read from [summarystats.ma].
Phenotypic variance estimated from summary statistics of all 8131642 SNPs: 2.16654 (variance of logit for case-control studies).
Matching the GWAS meta-analysis results to the genotype data ...
Warning: can't match the reference alleles of 517394 SNPs to those in the genotype data. These SNPs have been saved in [test.badsnps].
Analysis finished: Tue Aug 26 13:18:13 2014
Computational time: 0:2:28
Error: all the SNPs in the GWAS meta-analysis results can't be found in the genotype data.
Can you help ?
Thank you.