When working with indels, this function replaces any variant with length >1 to N. Need to update to correctly handle longer strings.

I am a beginner in bioinformatics.
I don't know how to get the VCF file I need.
I look forward to your help.
Thank you for your help.

Example here:

http://www.schlosslab.org/mikropml/articles/parallel.html

When I read into to the guid of prewas, I saw that reference genome could be provided, but couldn't see how to specify my reference genome in the input of prewas:
results_maximal = prewas(dna = vcf,
tree = tree,
outgroup = outgroup,
gff = gff,
anc = TRUE)
How do I specify this? Is the genome detected in the vcf input file?
Thank you

Add vignette explaining how to use prewas

Rather than grouping all minor alleles together, which is the only option now.

Hi,
I am using R version 4.0.3 and trying to install prewas. However, it keep showing that it is not available in this version. Is there a repository CRAN that I could download from?

For the vcf file input, If I'm generating a matrix for 300 ~500 strains for input of TreeWAS. Is there a tool you would recommend for generating this input?
Thank you!
Christine

Possibly add to rownames after another pipe. Makes it easier to filter variant marix by different impacts.

Hi.

This is a friendly reminder that plan(multiprocess) of the future package is deprecated since future 1.20.0 (2020-11-03). It will eventually become defunct and removed. The background for this can be found in HenrikBengtsson/future#420.

Your prewas package relies on multiprocess, cf. https://github.com/Snitkin-Lab-Umich/prewas/search?q=multiprocess.

Please migrate your code to the platform-independent plan(multisession) or the Linux/macOS-specific plan(multicore). If you want to emulate what multiprocess does, you can do something like:

  if (parallelly::supportsMulticore()) {
    oplan <- plan(multicore)
  } else {
    oplan <- plan(multisession)
  }
  on.exit(plan(oplan))

BTW, if you don't already do so, please make sure to undo any plan() you set in your code, as illustrated by the above example. This is needed to guarantee that calling your code won't override settings that the user has set previously. You can read about this in https://future.futureverse.org/reference/plan.html#for-package-developers.

Thank you,

Henrik
(maintainer of the future package)

e.g. to collapse only predicted high & moderate impact variants into genes (excluding low impact variants)

Hi!
My Prewas wasn't able to be finished due to the following issue:

Looks like it's related to the future library? Could you please help me with it ?
I also wonder if there is a way to run prewas faster if I have a large vcf file (after vcfR it's around 6GB).
Thanks !

prewas(snpeff_vcf) fails to make a rooted and fully dichotomous tree.
Replace sample data to work better as example.