BQSR for RNA-seq
I am performing BQSR on RNA-seq data for the purpose of SNP calling. I was wondering about some issues:
My organism does not have a known set of SNPs. I asked this question before in the forum and accordingly, I am using a set of SNPs filtered as the input of knownsites for BQSR. In filtering, some SNPs have a tag 'SNPcluster', shall I use this file or shall I somehow filter the file so only the PASS SNPs are retained?
I have performed SNP calling only on a subset of my bam file because I was interested in certain chromosomes. Would that be fine if I only use this subset of SNPs and try to recalibrate only the subset of bam file not the entire bam? I am asking this question in case this can somehow create a bias for final results.
Thanks in advance for your help!