how can I use the BQSR result for further analysis

Question

[Learner]

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.

[finswimmer]

Hello Learner ,

have a look at my opinion about BQSR in A: Applying BQSR before running GATK's HaplotypeCaller on whole-genome sequencing d .

fin swimmer

[Learner]

@finswimmer Hello, Thanks for your comment.I have read that . I am not after words, as I was clear in my question let says I want to use that option then what ? how can I use it?

[finswimmer]

If you are at the end of the BQSR pipeline you have a new bam file. This one is the input for any further step.