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Take in the snpEff.config information regarding genomes and gene sets as a dictionary (e.g. key: GRCh38.81, value: tuple with genome fasta URL and GTF gene set URL)
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**Description of bug:**
Using [DamageProfiler 0.5.0](https://github.com/Integrative-Transcriptomics/DamageProfiler), I get a result file that breaks MultiQC, see below.
**MultiQC Error log:**
```…
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I ran this command line:
python bcbio_nextgen_install.py /mnt/e/bcbio/share/bcbio --tooldir=/mnt/e/bcbio --genomes hg38 --aligners bwa --aligners bowtie2
However, I got some errors during the instal…
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I am annotating a list of variants from the canine whole genome sequencings post filtering to retrieve significant candidate genes via SnpEff against the **CanFam3.1.99** database.
I ran the comman…
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I try to run viralrecon for 86 samples. It seems the pipeline gets stuck and I cannot figure out why. I did run the pipeline on my local machine (14 cores, 128 GB memory) with standard configuration l…
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Hi.
When I am running SnpEff with "len" option, I get the following error messages.
> java -Xmx4g -jar ~/tool/snpEff/snpEff.jar len -r 100 GRCh37.75
> java.lang.NullPointerException
> at >ca.m…
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Hello,
I built a database from my own genome, and checked that it was present on the snpEff server with:
java -jar snpEff.jar databases | grep -i Walnut
Walnut …
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[Nextflow](https://www.nextflow.io/) is a workflow execution manager and workflow specification language with a lot of nice features for developing and executing bioinformatics workflows (e.g. support…
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Hi,
Just a quick question. is it possible to set a path to the Tabix index file?
I have tried the following:
```python
from cyvcf2 import VCF
variant_file = VCF("vcf_file.vcf.gz")
variant_…
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Hello there 🙋♂️
This Action doesn't work very well with https://github.com/TGotwig/Awesome-Bioinformatics/tree/patch-2
The output is sometimes quite random from run to run and has always workin…