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# Poretools
- [ ] Add link to [readthedocs](https://poretools.readthedocs.io/en/latest/content/examples.html)
# SNPEff
- [ ] It is absolutely unclear how to use `SNPEff download` and `SNPEf…
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I am trying to use the beta functions
![image](https://github.com/smith-chem-wisc/Spritz/assets/21457/a4c3de3b-a926-4a0d-99c1-083b305ddcab)
but facing this error (log below), any ideas how to pr…
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**Describe the issue**
Can't download the databases of python bivittatus while using snpEff download, however I can download other speices' databases using same method.
**To Reproduce**
1. SnpEff…
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Hi,
I am trying to parse a vcf created by snpeff to get a maf file, but I get the following error:
[miguel]$ python /bmm/home/mj308/vcf2maf-master/vcf2maf/vcf2maf.py -v --maf par.realigned.bam.filte…
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### Ask away!
Hi, I have two questions:
1. I would like to know bamtats version you are using in the pipeline.
2. I am trying to load the different container image but I was only successful wi…
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### Description of the bug
Hi, I'm trying to use Sarek from the annotation step. I'm using Linux and Conda. Each time I try, it gives me an error like this:
ERROR ~ Error executing process > 'NFCO…
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**Version info**
- bcbio version (`bcbio_nextgen.py --version`):
```
$ bcbio_nextgen.py --version
1.2.9
```
- OS name and version (`lsb_release -ds`):
```
$ lsb_release -ds
"CentOS Linux rele…
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New installs of snpEff are getting java version 11 and snpEff requires java version 8.
When you run snpEff with java 11 it runs to completion but doesn't output anything, no error messages either..…
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Currently, we use "hg19" and "hg38" reference genomes (from UCSC) to produce snpeff annotations. The result misses "gene_id" field (the value is the same as "gene_name"). We can switch to use GRCh37 a…
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So everything has been working smoothly as far as alignment and variant calling up to this point, however, when I try to download the human snpeff database I get a make error. Here is the code:
gkn…