Hi everyone. I have 3 dataset (from 2 different illumina chips) that need to be merged. I did this using plink. When I first merged the first two dataset, everything was fine, from the p values to the QC tests. Everything was normal. Then I merged the other dataset and this is what happened: I checked the mind geno and maf with very bad result. Then I looked for the p_value and lots of SNPs had a p_value too low ( rs5648916 example. p value 3,8 *10-308).
I don't know what is wrong with this dataset.
Can someone help me please?
_have a great day
1 answer
I was expecting a very low correspondency, due to the fact that these dataset are made on 2 different illumina chip. The problem is that I don't know how to isolate the common SNPs among these merged files, in order to have a final dataset on which I can working on... Using mind geno and maf only tells me that the quality of those SNPs is bad. There is some other way to use these command?. and yes, the hh genotypes are all from X and Y chromosomes.
Thanks Christopher for your help.
I hope you are having a great day
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Since you are not announcing a tool this post should have been a question, I have adapted the post type.
Options in effect: --noweb --bfile BANGWAS3NOV2011 --bmerge besta_new2_1_1.bed besta_new2_1_1.bim besta_new2_1_1.fam --make-bed --out final_merge2018
Reading map (extended format) from [ BANGWAS3NOV2011.bim ] 657366 markers to be included from [ BANGWAS3NOV2011.bim ] Reading pedigree information from [ BANGWAS3NOV2011.fam ] 1758 individuals read from [ BANGWAS3NOV2011.fam ] 1758 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9
802 cases, 956 controls and 0 missing 1058 males, 700 females, and 0 of unspecified sex
Reading genotype bitfile from [ BANGWAS3NOV2011.bed ] Detected that binary PED file is v1.00 SNP-major mode Using merge mode 1 : consensus call (default)
618093 markers to be merged from [ besta_new2_1_1.bim ] Of these, 395002 are new, 223091 already exist in current data 479 individuals merged from [ besta_new2_1_1.fam ] Of these, 479 were new, 0 were already in current data
Detected that binary PED file is v1.00 SNP-major mode 2237 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss) Missing phenotype value is also -9
1281 cases and 956 controls Before frequency and genotyping pruning, there are 1052368 SNPs 2237 founders and 0 non-founders found
827140 heterozygous haploid genotypes; set to missing Writing list of heterozygous haploid genotypes to [ final_merge2018.hh ]
95420 SNPs with no founder genotypes observed Warning, MAF set to 0 for these SNPs (see --nonfounders) Writing list of these SNPs to [ final_merge2018.nof ]
Total genotyping rate in remaining individuals is 0.490581 0 SNPs failed missingness test ( GENO > 1 ) 0 SNPs failed frequency test ( MAF < 0 )
After frequency and genotyping pruning, there are 1052368 SNPs After filtering, 1281 cases, 956 controls and 0 missing After filtering, 1320 males, 917 females, and 0 of unspecified sex
Writing pedigree information to [ final_merge2018.fam ] Writing map (extended format) information to [ final_merge2018.bim ] Writing genotype bitfile to [ final_merge2018.bed ] Using (default) SNP-major mode
thanks for the quick answer
So over 60% of the SNPs in besta_new2_1_1.bim are not included in BANGWAS3NOV2011. Is this what you expected?
Also, what chromosomes are these on?
Please post up the log file for the final merge step