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?
You should merge them using the vcf-merge utility that is part of the vcftools package.
Concatenation would be appropriate if you had separate files for each chromosome, and simply wanted to join them 'end-to-end' into a single file. In this case, your SNPs and indels need to be inter-woven ie. merged.
If you haven't used vcftools before, you can find it here:
Specifically, you can read about vcf-merge here:
You will need to compress the vcf files with
bgzip and index with
tabix before you can run any vcftools functions on them.