Multisample vs Single sample(Paired sample MUT &WT separate BAM files)
I'm currently working with zebrafish mutants, and compare phenotypically wild-type and mutant siblings for mutations. I have 3 different mutants, like 3 pairs of different Mutant and Wild type siblings. e.g Mut A, WT A and Mut B, WT B and so on.
I called variants in Single sample mode, i.e. WT separate and Mutant Separate (GVCF haplotypecaller) for all the pairs (separate GVCF for each BAM file).
Then I combine all the samples to call Genotypes, to use all the coverage from other samples to get correct Genotype. So in the end I have a 6 sample VCF file.
Then just to check, I called Variants directly from Haplotypecaller with using just pairs, i.e Mut (A) and WT (A) together to call variants, only for one pair.
But, After comparing at some positions in same sample, say A, I'm seeing difference in genotypes, as compared in 6 sample VCF and my 2 sample VCF (of same mutant+sibling vcf). Even the DP is different in some cases.
I want to ask, which one is the better method ? I though multisample variant calling would be better.