I analyzed whole exome seq data from 5 mouse cell lines without matched normal. I used bwa -> GATK realignment -> GATK recalibration -> Varscan2 -> annovar for variant calling. I used GRCm38 as the reference genome. Three of these cell lines have much more (almost twice) non-synonymous SNPS than synonymous SNPs. Is that normal? I would expect more synonymous SNP in the data. The remaining two cell lines have more synonymous SNPs.
Thank you so much.