Rat's snpdb file
I would like to run mutect for Rat. is it essential to provide dbSNP file? Rat dpSNP file does not provide information on which is Somatic and which is germ line. All SAO=0.
Did mutect use germ line SNVs in dpSNP file to filter out germ line mutation from output.??If so, I think Rat dbSNP will not provide helpful information as many somatic mutations might excluded because of ambigius SAO flag
One more thing is that dpSNP file is in rn5 not latest rat assembly rn6.