I am wondering what everyones favourite tools are for checking kinship coefficients between individuals in family studies? I am doing this for QC on some projects where the results we were getting were not what we expected.
In this case I was using KING with plink formatted files that either came from genotyping data exported from Genome Studio or were generated from VCF files from exome sequencing data using vcftools (to convert from VCF to plink). In some cases the calculated kinship coefficients didn't match up, although some of that may be issues with filtering of variants in the VCF case.
What does everyone like to use for these tasks? Also do you have favourite tools for comparing SNPs from a genotyping experiment with your VCF files for quality control purposes?