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halSnps allows the extraction of snps declaring a refGenome and one or multiple targetGenomes.
The output is reported as below :
```
refSequence refPosition Scer Spar
chrI_Scer …
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LDtrait(
snps=snps,
pop = "ALL",
r2d = "r2",
r2d_threshold = 0.1,
win_size = 5e+05,
token = "my token",
file = FALSE,
genome_build = "grch37",
api_root = "…
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I have been using a core genome alignment as input of grapeTree stand-alone version, but it crashes when the alignment contains too many sequences because of a memory issue (I do not have enough memor…
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Hello, mim-tRNAseq maintainer,
When performing alignment with mim-seq, I encountered an error where the SAM file header could not be read. Strangely, this issue only occurs with some of the files. …
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Hello Isabella,
I'm writing to you because I have a few problems to install Amr++_SNP.
I mannaged to install in a python 3.12 version and didn't work because of pysam and a problem with wheel. T…
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When running `gdtools COMPARE -f TSV`, in frame deletions (here, Δ3 bp) are being recorded under the "genes_inactivated" column. I think "genes_inactivated" should only definitely apply to indels that…
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Hi @jamonterotena,
Thanks for the updated, that looks great.
I already tried out [haploRILs](https://github.com/GoliczGenomeLab/haploRILs) this morning.
The functions works for my d…
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### Operating System
Ubuntu 22.04
### Other Linux
_No response_
### Workflow Version
latest
### Workflow Execution
Command line (Local)
### Other workflow execution
_No response_
### EPI2ME …
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Right now, Poseidon is officially flexible with respect to the Snp-Set of the genotype files, but the archives are of course not. All public archives currently support only the 1240K format, or the HO…
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Hello,
I am trying to map my trimmed reads to a pseudo-reference sequence. I have seen that for phyluce versions 1.4 and 1.5 this was done using the snsp.py script and I have also seen that there us…