Brad Wubbenhorst

icon company University of Pennsylvania icon location Philadelphia icon location Chief Bioinformatician for the Nathanson Lab at the University of Pennsylvania Perelman School of Medicine.

Results 5 comments of Brad Wubbenhorst

negative BAF values estimating LOH

Hello, Im having a similar issue; negative BAF values and everything in cn2 is 0. I did not appear to have any issues generating the cnvkit calls. I ran PureCN....

negative BAF values estimating LOH

I tested with a vcf from a different caller, VarDict, and I was able to properly generate baf values. Im not certain why it worked; I do not know what...

Snp-pileup failed to return data

Im not certain if this is the same issue as the OP. I get some results from snp-pileup, but I only get chromosomes 1-9 and X. Any two digit chromosome...

BAF doesn't seem to be correct

Hello, I am also getting baf values of 0 when using varscan2 germline/loh calls. It happens for every tumor/normal pair in every segment. I do not get any errors or...

BAF doesn't seem to be correct

Oh wow, it is the missing AF column I think. I tried a different caller, VarDict, which has an AF column. The stdout changed to reflect breakpoints and the baf...