I am trying to generate VCF using full and split (by chromosome) BAM files by GATK but after successful completion, there are difference in the VQSLOD score:
For full : VQSLOD=-6.339e-01
For split : VQSLOD=-1.472e+00
Does this means splitting the BAM is not correct or is it because of wrong parameters? or it is correct and I can neglect this?