Kinship matrix in pcangsd

Rosemeis / pcangsd

Framework for analyzing low depth NGS data in heterogeneous populations using PCA.

GNU General Public License v3.0

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Kinship matrix in pcangsd #72

Open ThibauldMichel opened 1 year ago

ThibauldMichel commented 1 year ago

I am using PCAngsd v.0.95, and try to output a kinship matrix.

The kinship matrix command exist in PCAngsdv2 (-kinship): http://www.popgen.dk/software/index.php/PCAngsdv2

But I cannot find the option in PCAngsd: http://www.popgen.dk/software/index.php/PCAngsd

I guess the kinship matrix is given in a binary numpy format (file.npy), but the documentation is unclear on this subject.

Rosemeis commented 1 year ago

Hi,

The kinship estimation was unfortunately a prototype function that was never fully tested and has therefore been removed in the later versions. Sorry for the confusion!

Best, Jonas