MergeVcf and SortVcf in GATK4?
After variant calling by Haplotypecaller (gatk4) and hard filtering, I merged snp and indel vcf files using MergeVcf that suggested here instead of using CombineVariants in gatk4. But, I found the variant count in the merged vcf file isn’t the sum of variant count in the snp and indel vcf files. So, I tried SortVcf, which generated a merged vcf file that the total count of variant in this merged vcf file was the sum of the counts in the snp and indel vcf files. As I found, SortVcf doesn’t resolve the overlapping snp and indel, unlike MergeVcf, yes, is it right? If it’s right, could you please let me know which type of variant (snp or indel) take precedence in merged vcf file and why?
Also, please kindly tell me which one (MergeVcf or SortVcf) do you suggest and why?
Thanks in advance