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Doubt Regarding Combine Variants and Multisample SNP calling
I used GATK combine variants to call SNP from my 7 vcf files. Now I am using unified genotyper to call all samples simultaneously for SNP.
When I focused on my gene of interest (DLX6), in combine variants output, there are 5 "./." among 7 samples. but in case of multisample SNP calling, DLX6 gave 0/0 in those samples and its corresponding information. So, I want to know what is the meaning of "./." in combine variants results and which results should I take for analysis?