Calculate the kinship matrix from NGS data

Question

[Begonia_pavonina]

I wish to calculate the kinship matrix from a batch of Next Generation Sequencing (NGS) data.

Previously, I have tried to use PCAngsd 0.98 to output the matrix, but it seems that this option does not exist any more since the previous version of the software PCAngsdv2.

http://www.popgen.dk/software/index.php/PCAngsd

http://www.popgen.dk/software/index.php/PCAngsdv2

Would anyone know what softwares could be used to get a kinship matrix from genomic data files (BAM, VCF) or from genotype probabilities files (BEAGLE, NUMPY)?

Answer 1

[chrchang523]

plink2's --make-king-and-make-king-table commands can be used to compute a kinship matrix from a VCF.

Sample usage: plink2 --vcf my.vcf --make-king-table