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Pankaj suggested that we annotate the variants from this combined VCF file: http://datacommons.cyverse.org/browse/iplant/home/shared/terraref/genomics/derived_data/bap/resequencing/danforth_center/ver…
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Hello IUC,
**Tl;DR:**
Help us fix tool tests!
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we would like to make sure that our tools are well tested and working in the widest range of deployment scenarios possible…
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### Description of bug
### Failure
When using multiqc (v1.10.1) on multiple FastQC reports generated from fastq files named as follows:
`^[a-zA-Z]+\.[a-zA-Z]{2,}_[12]{1}\.fastq\.gz`
e.g.
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Hey all, I am working on Somatic CNV calling and wanted to try out CNV_Radar.
I ran into some issues though while testing with a single sample.
I installed CNV_Radar locally, and ran following com…
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Hi,
Lancet generates in output the list of variants in VCF format (v4.1). All variants (SNVs and indels either shared, specific to the tumor, or specific to the normal) are exported in output. Follow…
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Is there an hg18 database for SnpEff? thanks
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Hi,
In Debian we are very much willing to package SnpEff, as many other wanted software depend on it.
Yet, the last release (v4.3t) is missing copyright header in all .java files and also a file…
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Dear There @snpEFF,
We process large number of isolates of a virus, daily, and produce an annotated vcf using snpEff. Now the numbers of samples are reaching 300,000 and it is taking more than half…
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ncov-tools v1.3 runs snpEff, which creates two output files at the top-level of the ncov-tools output directory. We currently aren't publishing those to the `--outdir` in this pipeline.
Publish the…
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For reproducibility, we need to convert shell commands to wrappers where they exist.