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Merging VCF files, keeping reference alleles
I have in a database 11 vcf and bam files for individuals we've sequenced. I have been trying to merge the 11 individual vcf files into one combined vcf file using CombineVariants in GATK. While it does combine the vcf files, it does something odd that I'm sure has been solved by other users and I am looking for input on.
A singleton SNP in individual 1 will be given "./." in all other 10 individuals instead of "0/0". Is there a way to fix this--the genotypes are not missing, they are reference.That said, some of them will be missing and are rightly called "./.", but I don't know how to incorporate this information into a merged VCF file.
Your help is most appreciated and apologies if this has been asked before--I couldn't find this exact topic.