We have SNP array data and whole exon sequencing based SNP calling results for the same group of samples.
Now we have genotype data in VCF format from both techniques. The samples are the sames. But the list of SNPs can be different, with some overlapped SNPs from both data.
We want to merge the VCF files (of genotypes) by array data and whole exon sequencing. We wonder whether there are some tools can do this for us (e.g., vcftools). Especially, in our case there are about 26k SNPs whose genotype were called by both array and whole genome sequencing data. And for those overlapped SNPs, I think there must be some genotypes were called differently by two techniques, for certain SNPs and individuals. So I also concern how to deal with the inconsistent genotypes calling when merging the two VCF files.