Entering edit mode
12 weeks ago
am29
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60
I am trying to produce an MDS plot of 1000 genomes individuals and individuals from my dataset to infer the ancestry of individuals in my dataset. However, after merging the files and running --genome command in PLINK, my .genome file is full of NaN values, and looks like this:
FID1 IID1 FID2 IID2 RT EZ Z0 Z1 Z2 PI_HAT PHE DST PPC RATIO
0 1000g_sample_1 0 Mydataset_sample_1 OT 0 nan nan nan nan -1 nan NA NA 0
When examining the genome file, distances are calculated for individuals from 1000 genomes, but none are calculated for individuals in my dataset.
What could be the reason/solution for this?
