flashton2003

Hi Fritz, I thought you might have come across this issue, it seems quite common in my data. Perhaps these repeat regions are susceptible to indels? I'm using v1.0.11, which...

Ah, no worries. Any thoughts on alternative filtering criteria, other than AF, which might help us include some of these ones?

@pd3 @tseemann @johnlees did any of you end up with a script to convert GFF3 to bcftools csq compatible Ensembl GFF3?

Thank you @pd3! If I roll my own I'll post it here at least.

This is my script. Takes a gff converted from gbk with the BioPerl gbk2gff3.pl script. Outputs something which can be used by bcftools csq. It's probably only useful as a...

You're welcome! On Mon, Sep 7, 2020 at 6:02 PM Petr Danecek wrote: > This script has been now added, thank you @flashton2003 > > > — > You are...

Thanks both!

In terms of the environment etc, sorry should have mentioned, it's running in a fresh conda env. PySeer v1.3.4. Other packages installed in the env ```# packages in environment at...

Hi @mgalardini, ok I've done that. First thing, not quite sure if this is the intended output of pytest command? ```$ pytest -v tests/ going into /home/ubuntu/pyseer-master/tests no test dir...

I've re-run with `python pyseer-runner.py` and the first few lines are the same as just using the `pyseer` executable.