Calculate kinship coefficient for set of samples in VCF

calculate-kinship.sh

#!/bin/bash

bcftools norm -Ou -m -any $1 | # Split multi-allelic alleles
        bcftools norm -Ou -f /resources/hg19/ucsc.hg19.fasta | # Normalize
        bcftools annotate -Ob -x ID -I +'%CHROM:%POS:%REF:%ALT' | # Replace IDs with unique ID                                                                                                    
        plink --bcf /dev/stdin --keep-allele-order --double-id --allow-extra-chr 0 --make-bed --out variants                                                                                      
                                                                                                                                                                                                  
king -b variants.bed --kinship --prefix kinship                                                                                                                                                   
king -b variants.bed --individual