Nate Olson

You can run `hap.py` using `--engine=vcfeval` if you have `rtg-tools=3.10.1` bioconda package installed in the same environment, e.g. https://github.com/snakemake/snakemake-wrappers/blob/master/bio/hap.py/hap.py/environment.yaml. I'll let @mbargull, from the Bioconda team, chime in about adding...

@jkalleberg Sorry for the slow response. I think the current rtg-tools version works. Previously versions after rtg tools 3.10.1 were not compatible. However, I ran happy following conda env file...

hap.py wasn't developed for benchmarking SVs, you might want to try Truvari (https://github.com/spiralgenetics/truvari/wiki) or Svanalyzer (https://svanalyzer.readthedocs.io/en/latest/) as they were developed specifically for benchmarking SVs.

Thanks for your responsiveness and for working to update the hap.py bioconda package and hap.py/pre.py wrapper. We use the main hap.py function, which does the comparison and calculates performance metrics,...

Here is my first attempt at making a wrapper for the main hap.py command. https://github.com/nate-d-olson/snakemake-wrappers/commit/34e7de271a9cc14546f51436d9f8986d04935813 I had a few questions regarding recommendations/ best practices for creating wrappers. 1. Defining default...

@jafors and @johanneskoester thank you for your help with the hap.py bioconda packages and snakemake-wrapper. Now that we have a dipcall bioconda package I wanted to start working on the...

@vsoch Thank you for the quick response. Unfortunately, all the repositories or https://gitlab.nist.gov/gitlab, are not publically accessible as this gitlab instance is hosted on an internal server. I am happy...

@vsoch and @cpauvert https://gitlab.nist.gov/gitlab/njd2/giab-asm-bench-whole-genome is behind an internal firewall and password protected. This is probably a rare use case. I am happy to help with testing but think implementing functionality...

@vsoch sorry for the back and forth. I cannot create an open GitLab.nist.gov repository. I set up a free gitlab account and want to set up a snakemake repo for...

@vsoch here is the repo I set up for testing, https://gitlab.com/natedolson/snaketestworkflow. I am happy to run some tests myself or help you setup a testing framework using this example public...