I am newbie in Haloplex data analysis. I have haloplex data from few tumor and normal samples. I mapped them by BWA and did not remove duplicates reads as suggested by the company. I called variants with mpileup.
Now I am wondering what threshold I should put in terms of variant read depths and allele frequencies to say that the detected variants is true and not an artifact? I know my question is very general but any input is highly appreciated.
Also, What statistics do you give for haloplex data?