Dear all hi,
I would like to know if you guys could help me about starting calling somatic mutations with somaticseq. Right now I am overwhelmed with the data and the program that's why I cannot produce data.
My biggest problem is I am not sure how can I create a new classifier. Should I use the data that was studied in the paper as a ground truth? or directly start off new with my current data.
As I understand from the manual, I have to call mutations with individual programs first. After that I will combine the outputs of the individual callers by somaticseq to create a classifier. Then call mutations with somaticseq algorithm? Once I created this classifier, I don't have to redo the creating classifier part. I have to only call the mutation with created classifier.
I will be working with the data from ICGC and TGCA thats why I have to create a robust pipeline. Since my data is too big, I am confused about the part where I create my classifier. How can I build a classifier which will give me true results for my data which is consisted of +250 samples including tumor and normal pairs?
Any information will be valuable for me. If there is someone who has used this program before PLEASE HELP ME!