Hello,

I'm trying to perform HapMap PCA, after which plink bails and gives me the following message:

ERROR: Stopping due to mis-matching SNPs -- check +/- strand?

In my script I do the following to try and rectify this.

# initial merge study and hapmap data                                                                                           
plink --bfile ${DATA} --bmerge ${HAPMAP_DATA}.bed ${HAPMAP_DATA}.bim ${HAPMAP_DATA}.fam --make-bed --out clean_data/hapmap_pca/dataset/${NAME}_HapMap3_pruned

plink --bfile ${DATA} --flip clean_data/hapmap_pca/dataset/${NAME}_HapMap3_pruned.missnp --make-bed --out clean_data/hapmap_pca/dataset/${NAME}_flip

# merge study-flip and hapmap data                                                                                              
plink --bfile clean_data/hapmap_pca/dataset/${NAME}_flip --bmerge ${HAPMAP_DATA}.bed ${HAPMAP_DATA}.bim ${HAPMAP_DATA}.fam --remove clean_data/exclusions/sample.exclusions --extract clean_data/indep_snps/independent-0.05.snps --make-bed --out clean_data/hapmap_pca/dataset/${NAME}_HapMap3_pruned

After which I still get the same error.

I perform --flip-scan on my dataset, but I just get NA for NEGSNPS for all SNPs. I think it is because I have a dataset that just has controls and not cases to compare against? Regardless, can someone point me in the direction of what I can do next to investigate this problem?

Thanks.