I have 3 vcf files containing 10, 15 and 20 different individuals in each file. The merging command "bcftools merge -0 --missing-to-ref", was used to merge the vcf files together. After merging, in a location of the merged vcf file, the genotype (GT) is changing to 0/3; whereas in the unmerged vcf file, the same GT was 0/2. In addition, variant-specific parameters (e.g. SOR, QUAL, BaseQRankSum, etc.) are also changing in the merged vcf file. This thing is happening for multiple variants in multiple individuals. This seems to be an issue for the downstream analysis.
Can anyone suggest me how to fix this issue? Also please let me know if there are other tools where I can merge multiple vcf files with different Individuals.
N.B: The version of bcftools I am using is 1.9.