Sigve Nakken

+1, I experienced the same issue. https://github.com/sigven/oncoEnrichR/issues/22

Eva, You may try a workaround using Conda, that worked for me, i.e. `wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh` `chmod 0755 miniconda.sh` `./miniconda.sh` `conda update conda` `conda install -c bioconda vt` regards,...

Hi @gudeqing, Thanks a lot for noticing this! Indeed a bug, pushed a fix to `pcgr.py` now. best, Sigve

Sure thing, if you have an example VCF that you think adheres to these parameters, I could do such a check. I would also need the assembly version (grch37 or...

Hi @gudeqing, Cool! Very nice small script for this purpose. Although I agree that retrieving this information directly from the FORMAT column would by far be most convenient for most...

Hi @gudeqing, I will follow up now on the great contribution you have done here. I am in the process of updating PCGR, and will be looking into how your...

Hi, Yes, that’s my experience previously. Underscores are not permitted in the FORMAT columns. You can disable the strict VCF-validator in the config file (PCGR is either way ignoring the...

Hi, By mistake I forgot to attach the default TOML config file in the pre-release, but it is present in the repo now: [pcgr.toml](https://raw.githubusercontent.com/sigven/pcgr/master/pcgr.toml). I suggest you download it and...

Hi @brentp, A minor follow-up on this one. When I run vcfanno (v0.3.3) on a VCF with _no_ `FORMAT` or sample genotypes (only the eight mandatory columns), the annotated VCF...

Just noticed https://github.com/brentp/vcfanno/issues/123, so this behaviour is already reported. Sorry for the duplication.