I have a vcf file of SNPs and another vcf file for my Indels. During SNP calling step by GATK, I created them separately instead of using -glm (calling together SNPs and Indels). Now to get the consensus sequence of my mapped genome, I want to put them together in the same vcf file. Should I merge these two vcf files or concatenate them to get the proper variant vcf file, so I can consider SNPs and Indels for my consensus sequence?
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