I have two questions concerning SNP calling using cancer cell lines:
Comparing two human genomes on average 1 in 1000 to 1300 nucleotides is altered. Does anymore have a similar number for cancer cell lines? I was wondering if anyone knows a study where multiple cell lines were compared - I am particularly interested in the number of common and unique SNPs between them.
Concerning the SNP calling process itself, what would you recommend to get all SNPs? Call with GATK HaplotypeCaller and Mutect2 in tumour-only mode? Then merge both results?