Lucas Czech

This is still an issue, and users of my pipeline are stuck due to this bug now, see [here](https://github.com/moiexpositoalonsolab/grenepipe/issues/66). Unfortunately, I cannot reproduce this myself, and hence not really help...

Hi @ribeirots, thanks for the suggestion - let's see if I am getting this correctly: > Would it be possible to have the max read depth be a percentile? For...

Hi @ribeirots, all right, just checked how PoPoolation2 is doing this - they indeed read the whole input data just to get those thresholds to get the value for a...

Also, I noticed the following in the wrapper: ```snakemake try: shell("curl -sSf {url} > /dev/null 2> /dev/null") except sp.CalledProcessError: continue shell("(curl -L {url} | gzip -d >> {snakemake.output[0]}) {log} ```...

And another related issue. I hope it's okay to report this here as well, as it's the same underlying problem, but in the variation wrapper "v3.13.6/bio/reference/ensembl-variation", see [here](https://snakemake-wrappers.readthedocs.io/en/v3.13.6/wrappers/reference/ensembl-variation.html). There, the...

More updates, hope that's okay. My current workaround for this instead of trying to assemble the URL within the wrapper, I just offer an alternative rule that uses a user-provided...

Hi @DuttaAnik, thanks for the suggestion! That seems like a good idea and is not overly complicated to integrate. Unfortunately, I won't have time for this right now, but I...

Hi @DuttaAnik, quick update: In one of my own analyses, I am now also running into the limitations of the current implementation with CombineGVCFs, and it seems that GenomicsDBImport is...

Hi @DuttaAnik, GenomicsDBImport is now implemented in [grenepipe v0.14.0](https://github.com/moiexpositoalonsolab/grenepipe/releases/tag/v0.14.0) as the default when calling with GATK HaplotypeCaller. Thanks again for the suggestion! All the best Lucas

Hope this helps you as well. Apologies for not having implemented this sooner!