Lucas Czech

Hi @pettyalex, that sounds like a useful addition! I think it makes sense to offer that as an alternative to specifying those files directly, yes. Looking at the links you...

Hey @pettyalex, implemented this now in [grenepipe v0.13.0](https://github.com/moiexpositoalonsolab/grenepipe/releases/tag/v0.13.0). I think that resolves this issue - if not, feel free to re-open or start a new one. Cheers Lucas

Hi @ospfsg, interesting. What exactly do you mean by > It crashed and the terminal closed by himself. Without any error message, the terminal just closes? That does not seem...

Hi @ospfsg, how are things going? Did the pipeline work now with a reduced data set? From what you described, I can only guess what has happened - but if...

Hi @ospfsg, ah okay. So, it seems you want to use freebayes for variant calling on pooled data? In that case, I'd recommend to have a look at our [preprint](https://www.biorxiv.org/content/10.1101/2022.02.02.477408v2)...

Hi Octavio, > I assume that the second sentence is about your experiment 2, but did you test the impact on the results of a "fake" low ploidy on the...

Hi @ospfsg, good question, and you are not the only one with a request like that. Unfortunately, Snakemake itself is not meant for these things where changes from the outside...

Hey @ospfsg, did you get it to work? If so, shall we close this issue? Cheers Lucas

Hi @ospfsg, okay, finally also implemented to start the pipeline from bam files now in [grenepipe v0.13.0](https://github.com/moiexpositoalonsolab/grenepipe/releases/tag/v0.13.0). It seems that this is an often-requested feature, so now it's finally there!...

Dear @RvV1979, indeed, that is a combination of features that is a bit tricky to implement, and I will unfortunately not have the time for that in the foreseeable future....