Comments (4)
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How does a PCA of the entire VCF file look like?
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Are the samples from one homogenous population or is there somekind of population structure?
The samples are from the 1000 Genomes CEU population. I believe it should be somewhat homogenous.
How does a PCA of the entire VCF file look like?
The vcf file contains nearly 100 CEU individuals + 5 samples that also come from the same region.
I haven't drawn the PCA (sorry!), but for a PCA of the CEU population (together with others):
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I actually used SNPS with a maf above 0.45 (high!). I will check if that might be the issue and let you know, inΕ.
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Related Issues (20)
- No output
- Problem with guess in emStep: 0.350616 0.350616 ... (unrelated to previous posts) HOT 8
- nIter = -1? Actually bestoptimll = -1? HOT 4
- verbose output HOT 3
- rmTrans option HOT 1
- extract_freq_bim error HOT 4
- Interpretation of relatedness (rab) coefficient HOT 4
- PL field in VCF HOT 4
- Add a LICENSE file
- possible to convert beagle to binary beagle (doGlf 2 to doGlf 3) or use beagle file as input? HOT 3
- Coverage HOT 2
- unexpected high theta values HOT 2
- [Question] Merging ANGSD Outputs HOT 5
- How does NgsRelate handle "missing data?" HOT 3
- Problem with guess in emStep: -nan HOT 2
- Bad results starting from beagle files? HOT 5
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- Issue with glf file - too many sites HOT 17
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