reported coverage zero #78
Description
Hi!
I am trying to run MSISensor-pro on some samples, and I am interested in shorter mononucleotide repeats (i.e., the repetition length is 8 or 9). I ran both scan and msi accordingly, so I use the parameters -l 8 -m 9 -p 1 for scan, and -p 8 -m 9 -x 1 for msi. However, scan reported also longer repeats, and msi shows zero coverage for everything. I know that it wants to find min 10 bp long repeats, because in the rare cases when my normal samples are already having an insertion in a 9bp long repeat, I have coverages.
My question is: what parameteres should I use? Thank you!