Markus Riester

Hi Stephany, 1) that's right, looks like the -500 off-target padding default is used. Out of curiosity, any reason you want to change this? I remember picking that cutoff after...

Yes, I recommend using the baits (not the exons, the actual capture baits) BED file as you got it from the vendor in IntervalFile.R. Then run Mutect with interval padding....

If you provide the proper baits file and use a 100-200bp padding in your variant calling, you shouldn't get much that's worth adding. It shouldn't hurt too much, but the...

Probably not super helpful me posting this since it's not supported yet, but compilation on arm64 fails for me here (both master and develop). ``` #0 4052.2 [ 61%] Creating...

Just tried my amd64 Dockerimage on my new M2 MacBook Pro, although on a Linux image. - Linux: bioconductor/bioconductor_docker:RELEASE_3_17 (Ubuntu 22.04) - GCC GNU 11.3.0 (default of that image) -...

Thanks @nalinigans. It compiled successfully last week, including the R bindings. Haven’t thoroughly tested yet. Any recent changes since then that I should try?

I think I fixed the crash in devel. Supporting multiple BQ fields is probably not something I will add anytime soon. The VCF standardization code is already quite a mess...

Yes, this is indeed a bug. The maf expected and observed are wrong with --model-homozygous.

Should be fixed in current developer branch. Will backport to stable in a week or two. Please let me know if you find other issues with cell line data.

Hi Jen. PureCN indeed does not adjust the tumor vs normal log ratio. All it is doing is a bit of cleaning up and alignment of on-target and off-target (which...