i would like to ask a more general question about exome sequencing, and mutation analysis. I have mainly analyzed transcriptomics data, so excuse me for any naive questions on this matter. I have some preliminary exome sequencing data (both fastq and bam files) from 3 patients:
in detail, i have for the same patients both whole exome sequencing data from CTCs (circulating tumor cells) and also exome sequencing data from biopsies of the same patients.
The main goal idea, is to find/identify if there are common mutational patterns (ie.SNPs) between circulating tumor cells and biopsies, which would be very vital for the time of diagnosis of the specific cancer, as also for the relative biological mechanisms, etc.
Perhaps an major issue is that there is no reference normal tissue (that probably limits the identification of somatic variants), as also the small number of patients-however, any ideas or suggestions about which tools or approaches i could implement for a putative variant annotation, or comparison, for this specific scenario ?
Thank you in advance,