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Hello,
We use instead of the normal workflow from snpir STAR pass-2 and the GATK best practises to create a bamfile. You recommend to use bwa-mem to align to the normal human reference genome to get …
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Hello,
I ran PhylotaR according to the tutorial, modifying it as is shown in the code below.
To create fasta files for each cluster I ran a loop in R. But when checking the sequences in the resu…
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The below line of example code in the README.md lists
````
import torch
from bpnetlite.io import extract_loci
from bpnetlite.io import LocusGenerator
from bpnetlite import BPNet
````
Howe…
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Hi,
I've got error when running:
`tsum 'apply(qm, 2, sort.int, partial = ti)': dim(X) must have a positive length
or
> 'if (qs < 1) {': argument is of length zero
To avoid the error I have…
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I see that typically gtc2vcf does a fantastic job in infering the coordinates with the SourceSeq mapping workflow. However, I note that in some cases when SourceSeq maps to different loci equally well…
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@gregorgorjanc @AprilYUZhang
I tried to use the true recombination rate to generate the transmission function of the second Baum-Welch implementation in the peeling cycle, and it turned out no improv…
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I have a problem,
I used DIYABC-RF, When running the simulations it tells me this:
!!! I have caught an exception which is:
Erreur dans readheaders().
Not enough loci of type found in the …
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Hello, I ran "selscan --xpehh --vcf vcf1_Chr1.gz --vcf-ref vcf2_Chr2.gz --pmap --out outfile", but no files were generated.
The result of the operation is:
selscan v1.3.0
Opening vcf1_Chr1.gz...
L…
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Thanks for developing this method. I've run into a potential bug where Ne estimates are different depending on the input file. I'm happy to share example files if that is helpful.
In short, given t…
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The assumption for things like `SomaticStandardCaller` (or others that use `pileupFlatMap`) is that `--loci` controls the loci at which to examine pileups. However, when using `CappedRegionsPartition…