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Could it be possible to choose the separator character for INFO field as list? Currently, the character "&" define a field as a list. Can we "add" characters? such as "," character?
These chosen char…
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**Describe the bug**
Hi, I'm trying ti install celescope and I found a problem during the instlation using conda
**To Reproduce**
```{}
source ~/.bashrc
cd CeleScope
conda create -n celescope…
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Hello,
I am having a problem loading a PED file into my gemini.db. I am using the following command:
gemini load -v /path/to/annotated/snpeff/vcf -t snpEff -p /path/to/ped /path/to/gemini.db
I am …
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Hey!
While working with our Nanopore data our goal was to use sniffles to extract BNDs annotate them using SnpEff and then design primers to verify some of them.
But when we started extracting seque…
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Hi,
When I use the following file as input to vcf2db:
[working.txt](https://github.com/quinlan-lab/vcf2db/files/1395206/working.txt)
the database is created as expected.
But when I use this …
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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### Description of feature
Hi,
I was wondering whether it is possible to integrate vcf2maf as well into sarek to directly convert annotated vcf files to maf.
https://github.com/mskcc/vcf2maf
…
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Hello,
I am trying to use snippy 4.6.0 via miniconda3 on Linux and the output given indicates my samples have 0 variants compared to the reference genome.
The created snps.csv has no data in it and…
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### Description of the bug
My latest Sarek run on normal-tumor paired samples for one patient using some tools (freebayes,mutect2,strelka,tiddit,cnvkit,controlfreec,merge) ended up with an instance o…
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I have a simple header reading error from markdup that caused my snippy to fail... I've pasted the log file below.
```### echo snippy 4.6.0
### cd /lustre06/project/6000186/congxu/snippy/A.rubrum
…