I'm starting my bioinformatics journey, and I have a basic question that you might be able to help with. Are the GATK programs for base quality score (BQSR) and variant quality score recalibration (VQSR) analogous?
I understand that they are designed for different steps in a pipeline and have different input filetypes, but overall they are both modifying the quality scores. Is one better than the other for SNP calling?
except for the name and that both are about probability they have nothing in common.
BQSR changes the quality values for each base within the reads which initially was set by the sequencing machine. The goal (or the hope) behind this is, that the new values are nearer to the truth. This changed quality values influences the mappibilty and alignment of the reads and - yes - have a bit of influence to the variant calling.
VQSR is a technique that tries to find out which changes in the sequences are true and are not some kind of artifact from the library prep, sequencing machine, bioinformatic pipeline, etc...