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Hi,
I am running sarek for the first time, and it is failing quite early. However, I'm not sure what the error is:-
```
WARN: Found unexpected parameters:
* --step-mapping: true
- Ignore this…
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The documentation for GATK's haplotypecaller says "This tool is able to handle many non-diploid use cases; the desired ploidy can be specified using the -ploidy argument". I am working with haploid ye…
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Hi,
I have a vcf file annotated by snpeff and want to extract "ANN[*].RANK" from the ANN field like
`ANN=G|missense_variant|MODERATE|TNN|ENSG00000120332|transcript|ENST00000239462|protein_codi…
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## Check Documentation
I have checked the following places for your error:
- [ ] [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting)
- [ ] [nf-core/sarek pipeline doc…
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An unexpected error has occurred.
Please consider posting the following information to the
conda GitHub issue tracker at:
```
https://github.com/conda/conda/issues
```
Current conda install:
```
…
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See this suggestion by @wm75: https://github.com/galaxyproject/iwc/issues/96
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C4:
* [x] bamUtil 1.0.15 (fails to install on Wynton?!?)
* [x] bat 0.18.3
* [x] bcftools 1.13 + add link to GitHub
* [x] blast 2.12.0
* [x] bowtie 1.3.1
* [x] bowtie2 2.4.4
* [x] cell…
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**Describe the issue**
When using maftools trinucleotideMatrix function, I got an error in "Extracting +/- 20bp around mutated bases for background C>T estimation", hg19 contigs were used and I chec…
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Hi!
Q1: Is there a reason that bcbio still uses salmon v1.4.0?
```
[2022-01-21T01:55Z] Version Info: ### PLEASE UPGRADE SALMON ###
[2022-01-21T01:55Z] ### A newer version of salmon with importan…
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- bcbio version 1.2.3
centos 7
I was attempting to run the workflow with PureCN.
A few minor fixes I had to make to get to this point:
> Update cnvkit to 0.9.7beta ( see https://github.c…
waemm updated
2 years ago