Kishwar Shafin

@yifeng-evo , * The variant in position `216` is a PASS variant with `GT` of `0/1` which means it's a het variant. * The variant in position `239` is a...

@yifeng-evo , There are a variety of things that go into the determination of a site being a true variant or not. Including base_quality, mapping_quality, strand_distribution etc. What it means...

@infotmatician , Can you please put down the full command you are running? I think the `--region` is causing this.

@infotmatician , It looks like a permission issue now. Can you please specify the `pepper_output/` to a directory that you explicitly mount with `-v`? For example use `/inputs/pepper_output` to make...

hi @BrendaLee1 , Can you please try to install pysam independently to see if you can install pysam? ``` python3 -m pip install pysam ``` If this doesn't work due...

@LiShuhang-gif , 1) We currently don't have a CLR SNP calling model in production. 2) The UL reads show work similarly well as the non-UL reads. In fact, all of...

@liuzhen51032 , I think this is coming from htslib, are you able to independently install htslib successfully on your system?

hi @liuzhen51032 , Sorry for dropping the ball on this. However, did you make sure to install all required libraries as suggested: ``` sudo apt-get -y install cmake make git...

@iiSeymour and @noncodo , I have recently implemented multi-GPU support for HELEN (https://github.com/kishwarshafin/helen), both training and inference. You'd have to switch to `DistributedDataParallel`. The `DataParallel` implementation we had was a...

I remembered I have multi-GPU functionality for bonito: https://github.com/kishwarshafin/bonito/blob/nanoporetech-master/bonito/basecaller_distributed.py