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Post by blinghu on Jan 17, 2017 20:06:58 GMT
Thanks so much for the GCTA tool, really a wonderful resource. My sample size in .ma file is greater than SNP count, but I still got the following error, could you please help?
I have got an error for running GCTA as below:
Error: too many SNPs. The number of SNPs in a joint analysis should not be larger than the sample size.
Options: --bfile EUR_AllChr.phase3_V5a_norm.7 --chr 7 --maf 0.01 --extract chr7.40.condional_analy_snplist_maf001.rmSampleSize0 --cojo-file ma_file_conditional_analysis_input.rm_sampleSize0.tab --cojo-joint --out chr7.40.condional_analy_snplist_maf001.rmSampleSize0.out
log file regarding snp count: Calculating allele frequencies ... Filtering SNPs with MAF > 0.01 ... After filtering SNPs with MAF > 0.01, there are 3329 SNPs (436 SNPs with MAF < 0.01).
sample sizes in .ma file -bash-4.1$ mo ma_file_conditional_analysis_input.rm_sampleSize0.tab SNP A1 A2 freq b se p N rs2326918 a g 0.8441 -0.0083 0.0097 0.3887 471990 rs186244095 a g 0.9994 0.3533 0.3087 0.2524 180659 rs7929618 c g 0.1378 0.007 0.0102 0.4925 472815 rs66941928 t c 0.7972 0.0057 0.0094 0.5468 473380 rs151222586 a g 0.9936 0.0535 0.0606 0.3772 374210 rs6039163 t c 0.0038 -0.0093 0.0632 0.8827 374210 rs146253013 t c 0.0052 0.0177 0.0572 0.7563 374210 rs6977693 t c 0.8504 -0.0099 0.0099 0.3153 472986 rs12364336 a g 0.8681 -4e-04 0.0104 0.971 472090 rs7190157 a c 0.3709 -0.0022 0.0073 0.7655 472712 rs148258120 t c 0.9993 -0.0685 0.1337 0.6083 374210 rs12562373 a g 0.7522 0.0031 0.0081 0.699 473380 rs142545482 t c 0.9996 -0.0681 0.2889 0.8137 173677
Many thanks,
Bolan
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