I am reading about this function which leads to a better variant calling. but I just don't know what to extract from it and give it to GATK ?I know that BQSR from the Broad’s GATK allows you to reduce the effects of analysis artefacts produced by your sequencing machines. It does this in two steps, the first analyses your data to detect covariates and the second compensates for those covariates by adjusting quality scores.
My question is that Okay, Now what should I do with those information or how can I use them?
is you could give me some idea it would be great.