I am a bioinformatics newbie analysing MAF file format data with
n_depth fields. My understanding is that low read count values for these fields are undesirable (false positives, lack of accuracy,etc). Is there a standard technique or process to establish a
cutoff value to exclude data with read counts below that
I use R for this work, so an R package solution would be ideal, but happy to do it another way if required.
Update: I would appreciate being updated if this is such a stupid question that it's not worth answering. Hard to know if you are completely wrong sometimes.