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# Doubt Regarding Combine Variants and Multisample SNP calling

Member Posts: 8

Hi sir,
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?

Tagged:

• Member Posts: 8

Hi sir,
I have attached my gene of interest DLX6 results came from combine variants and Multisample SNP calling. please look the DLX6 variants information in 7 samples. It's a two line results, so won't take your much time.

• Member Posts: 8

Hi sir,
Thank you for your reply. It clears my doubt regarding homozygous calls that are not coming in combine variants. But, there is some inconsistency in two of my samples. Younger son and wife sample contain heterozygous calls and satisfy other criteria (from multisample SNP calling),but it won't coming in combine variants results. I have attached my file and highlight the inconsistent samples in yellow. so please go through it once and let me know what's the reason for that inconsistency.