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### Description of the bug
We have run Sarek pipeline v3.1.2 on 3 WGS batches, including around 2500 samples, using the GATK.GRCh38 reference genome from iGenomes and mostly default parameters (see t…
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Should we be running simulations for (sub)regions where we haven't got any case data in the database? The case data is used for two things: displaying actual values against those projected by the mode…
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## Research question(s)
- Can we create a brain parcellation using data from pre-adolescent subjects?
- How similar/dissimilar is this parcellation compared to an adult parcellation?
## Descript…
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Hello again!
I have run your software on both the sample and some of my own. And I am a bit confused about some of the data in the output files:
1. In clean_cnv, are the cnv scores computed log-…
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Hi,
I noticed that when using 'sfm' mode, elprep uses more resources than allowed (e.g. all available threads instead of the given thread count). When using `filter`, this does not occur.
Cheers…
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Hi ,
I am new to this field and I am currently working on my master's thesis, focusing on the evolution of a specific morphological trait., I've opted to analyze 60 genes across a smaller number of…
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Dear HMF team,
I am trying to run SAGE v3.3. on a pair of tumor-normal whole-exome sequenced.
Below is my command
```
#!/bin/bash
# Ref fasta
fasta="../resources/Homo_sapiens/GATK/GRCh38/…
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Dear Authors. Could you clarify please.
Is there a stronger threshold for the identification of eukaryotic viruses? Because those contigs, which according to the program belong to eukaryotic viruses …
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Folks occasionally but consistently ask for this information on the forum and our current answer is that we provide these files as is. For the new GATK4 documentation, which we plan on releasing on Ja…
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> If I understand correctly the idea behind these metrics are taken from "rethinking semantic segmentation evaluation" paper, but could you explain to me how could I obtain AP,TPs,FPs,FNs for instance…