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Genetic PCA from poolseq genotype file
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18 months ago
AP • 90

Hello,

I have a sync file extracted with Popoolation2 software that looks like that:

Contig    Position  Ref    Pool1           Pool2           Pool3           Pool4
SCAFOLD1    11722   A   330:0:0:0:0:0   315:0:0:0:0:0   334:0:0:0:0:0   111:0:0:0:0:0
SCAFOLD1    11723   T   0:330:0:0:0:0   0:316:0:0:0:0   0:334:0:0:0:0   0:111:0:0:0:0
SCAFOLD1    11725   T   0:327:0:0:0:0   0:314:0:0:0:0   0:329:0:0:0:0   0:111:0:0:0:0
SCAFOLD1    11726   A   330:0:0:0:0:0   314:0:0:0:0:0   332:0:0:0:0:0   111:0:0:0:0:0

Each cell contain the allelic counts for each basis (e.g. 330:0:0:0:0:0 for A:T:C:G:N).

I would like to perform a genetic PCA on this dataset just as one would do it on a 012 file extracted with VCFtools. I guess, one could convert the sync file with a single value per cell by adding the total number of non-reference alleles and work from that.

Does anybody have experience with that? Any opinion/comment would be very helpful.

Thanks!

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