Variant Calling for one gene - Stage of filtering

Question

[andrebolerbarros]

Hi everyone,

I am interested in looking at variants of just one gene from RNASeq samples. For that, I am going to use the best practices from GATK for cases like this.

However, I was wondering: should I filter the bam files right after the alignment step and proceed with the pipeline with only the sequences for that gene or should I only filter in the VCF? Or at a different stage?

Thanks in advance!

André