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Hi Brad/Rory,
Running med-high coverage (~150x) tumor/normal exome calling with multiple callers (varscan, freebayes, + trying vardict for the 1st time) -- it looks like vardict is moving _much_ slow…
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Need to change the paradigm with filtering reads. Each base calling algorithm like `launch_freebayes` or `launch_varscan` should filter their own reads before output.
Also need to remove `vcf/unfilt…
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Hi,
I am trying to add indelcaller to my yaml file, but I got the error message,
Traceback (most recent call last):
File "/bcbio/bin/bcbio_nextgen.py", line 216, in
[2014-09-22 19:00] Checking sa…
ghost updated
8 years ago
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implement varscan
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Hi-
I've managed to install bcbio but am having some trouble with the test suite. There seem to be issues with freebayes and perhaps also with gatk. I just installed bcbio and then upgraded with bcb…
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Hello,
I tried to upload a VCF file (3.7 MB) which has caused _Failed: Bad Request (400)_ with the following Dockerfile:
```
FROM bgruening/galaxy-stable:dev
MAINTAINER auto script
ENV GALAXY_CONFIG_…
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Hi,
I am trying to compare the performance between freebayes and varscan. I found it takes less than 10 hours to finish variants calling by freebayes on a 32 cores + 60GB RAM machine, but when I run …
ghost updated
10 years ago
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It seems that the output VCF from varscan in bcbio-nextgen can not be used further for VarScan.jar somaticFilter?
java -jar /usr/local/share/java/varscan/VarScan.v2.3.6.jar somaticFilter 2your-arbitr…
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do some research on how much time each procedure takes on whole-genome data
If picard is too slow, we should just switch to samtools to further improve speed; it seems that picard takes a lot of time…
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# The README file is basically a command line manual that is copied from 'seqmule' command itself.
- I will write a new README.md file using GitHub markdown.
- Yunfei does not need to worry about it.