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Popular or notable formulae can be migrated to [Homebrew/core](https://github.com/homebrew/homebrew-core).
Bioinformatics formulae can be migrated to [Brewsci/bio](https://github.com/brewsci/homebrew…
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I have a PR coming for the reheadering which will fix the vcf reheadering. I am however getting this error:
```
[varscan.snp.genome.wustl.edu.TCGA-W5-AA33.vcf] VCF header validation error: SAMPLE hea…
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I have created ma file starting from mutect2 smatic vcf using vcf2maf. Seem works. I concatenate 6 maf on a single file and I import on maftools.
When I try to do this plot
```
`plotVaf(maf = la…
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Dear stuff in Boevalab,
I am in trouble when i run freec to analysis my WGS data. The problems is :
"Warning: control length is not equal to the sample length for chromosome M
Segmentation faul…
moshl updated
6 years ago
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I have run this command
```
/opt/bcbio.variation.recall/bcbio-variation-recall ensemble -c 1 -n 1 out.fg.gz /home/maurizio/database/hg19_primary.fa mutect2/436.mutect2.vcf.gz 436.varscan.all.Soma…
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Use of GATK is currently encumbered by a license that prohibits redistribution. We should consider replacing GATK with other tools that have more permissive licenses, so we can package viral-ngs for d…
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ONC31-02-EK5562-1737688
This sample shows EGFR c.2235_2249del 4.15% an c.2252C>T 4.15% on Varscan
This is in exon 19 and likely to be an indel
The Vardict VCF has been uploaded and the indel is n…
nfoot updated
6 years ago
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Hi Christoffer,
More of a question than an issue. I'm trying to run the superFreq with the variant calling that you suggested in your manual. Here are the commands that I use (which essentially fol…
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Because the output of `wc` is slightly different depending on the platform (linux/mac) or flavour (ubuntu, debian, etc.). The test does fail even if the job executes correctly, because it is checking …