Jens Luebeck

Hi, I am also wondering if there are any plans to generate the blacklist file for GRCm39? Thank you!

Hi, at this time only hg19, GRCh37, GRCh38, and mm10 are supported. Providing additional support for references of other species requires the construction of an annotation database. Unfortunately that process...

Which species do you have in mind? As mentioned above, the process is complicated and involves annotations from many sources. There is not a relatively simple way to do it.

The AA genome annotations are used for marking low complexity, repetitive regions, low-mappability regions, oncogenes, as well as areas that show high signal across many "normal" samples. You would need...

Hi, (1) Some very complex samples may take a long time to finish (possibly up to 2 weeks), however that is very rare. Typically reasons for long runtimes involve how...

Hi, 1. Thanks for the clarification. To produce your own data repo with hg38 + virus, take the original hg38 data repo, then replace the reference fasta, and .fai files...

Hi, Thanks for sharing this error. It is possible this is related to your mosek installation. A few questions: 1. What was the exact AA command you ran? 2. It's...

Hi, I believe this issue is because the docker image has not been updated to the very latest version of AA. Can I ask which fork you are using (virajbdeshpande...

Hi, Thanks for reaching out. If you apply [AmpliconClassifier](https://github.com/jluebeck/AmpliconClassifier) to your AA outputs, one of the output files summarizes the discovered SVs (see the [sample_name]_SV_summaries directory in the AC outputs)....

Hi Jennifer - thanks for this question - yes, you will need the cnv_prefilter when giving your own calls. The difference is this: `cnv_prefilter.py` - check if copy number gains...