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Can you share what steps you take to generate the vcf's, i.e. from after you run variant calling?
I.e. do you run haplotypecaller, then VQSR, then SnpEff, and if so, with which settings?
It woul…
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```
⚡ brew update
Already up-to-date.
⚡ brew doctor
Your system is ready to brew.
```
```
brew install ffmpeg --with-faac --with-fdk-aac --with-ffplay --with-fontconfig --with-freetype --with-frei0r …
ibaaj updated
6 years ago
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(mykrobeenv) [appbuild@ai-submit1]» pip freeze
biopython==1.70
easybuild-easyblocks==2.9.0
easybuild-easyconfigs==2.9.0
easybuild-framework==2.9.0
future==0.16.0
ga4ghmongo==0.0.1.2
mongoengine…
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Hi,
When trying to install on OSX I get this. Can't figure out what to do next.
```bash
10:54 $ perl INSTALL.pl --NO_HTSLIB
Hello! This installer is configured to install v87 of the Ensembl …
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Hello,
I did see the posting relating to this at: [https://github.com/Ensembl/ensembl-vep/issues/33](https://github.com/Ensembl/ensembl-vep/issues/33)
Unfortunately I wasn't able to get a solution…
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Hi Brad,
just a quick question. Is there a reason you omitted some VEP annotation options during that step?
Wouldn't it be possible to just use the "--everything" option to maximize the annotations …
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Hey,
I am trying to set up _genotype_ with your example data, but keep on getting this error:
[14 May 2016 00:48:13-MUD][memory] We made 20 allocs
[14 May 2016 00:48:13-MUD] Done.
[14 May 2016 00:48…
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Screened all Versions of OXA by inserting them into the reference genome ecoli_K12_MG1655_ref and generating error-free paired end reads with wgsim. Then the simulated reads were genotyped with atlas …
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I need to dig through the source, but I am seeing empty columns for everything except ExAC_AF. The source ExAC VCF is directly from the ExAC download page.
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We should explore whether it might be better to use:
The --pick option to give one effect per variant;
The --fields option to output the data as a csv.
A script to perform allele specific anal…