ive been trying to use varsacn on my pileup file in Galaxy
in the results, i get "N" in the reference column
I guess that it probably has something to do with the way the chromosomes are specified in the fasta of teh hg19 and in my data.
how can i see teh reference fasta file that is used by VarScan in Galaxy?
Or - do you ahve any other idea of why i get the Ns as the reference?
Many Thanks for your help