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What would be done is adding the flag SOMATIC to all VarScan mutations flagged with SS=2 (SS is Somatic Status) in the INFO field. For FreBayes, this would mean grabbing the records with VT=somatic an…
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Hi I keep getting stuck during the installation. After you fixed it by removing a bunch of unsupported packages the other day I tried it again. It got stuck but I managed to get it further along by…
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Hi Brad,
Recently I keep running bcbio with two whole genome sequence samples with 50X on AWS virtual machine (32 cores + 60GB RAM). It takes 4 days for mutect + scalpel to process 4 chromosomes. I c…
ghost updated
10 years ago
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We assume that the AD info field will be a variable length number of values as can be seen [here](https://github.com/cbmi/varify/blob/c4273706b0350460c90d6666b54f4847b4839caf/varify/samples/pipeline/u…
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I'm getting the following error with VarScan:
```
[2014-06-05 13:04] Calculating variation effects for tumor, mutect
[2014-06-05 13:04] Filtering for tumor, mutect
[2014-06-05 13:04] Finalizing varia…
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Hello Brad,
bcbio-nextgen gave errors when using with varscan on normal-tumor pair data.
File "/usr/local/share/bcbio-nextgen/anaconda/lib/python2.7/site-packages/bcbio/variation/samtools.py", line…
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Hello,
I have been working to run the cancer/normal example using the new AWS
cluster code. This time it went pretty smooth for the first three
hours. Then it silently stop. There was no final result…
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Hi,
I get an error when I try to import a multisample (n=10) VCF file into gemini (v0.8.0) on Ubuntu Server 12.04. The VCF was generated using VarScan v2.3.6 and annotated successfully with VEP.
Sin…
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I would like to try VarScan for my variant calls. Is varscan already included by automatic installation? or do I have to do:
bcbio_nextgen.py upgrade --tools --toolplus varscan=/path to varscan.jar
…
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This is a meta-issue to track what's left to make VCF files produced by different callers interchangeable.
- [x] Add `SOMATIC` flag to FreeBayes
- [ ] Convert `FA` to `FREQ` in FORMAT fields of MuTect…