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I noticed that Freebayes now supports somatic/tumor calling. I think, given it's a fairly mature tool, that support should be implemented in the pipeline
This is of course related to issue #112.
Giv…
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Hi, I am new to bcbio-nextgen. Please bear with me if my question sounds silly.
I installed bcbio-nextgen on my laptop based on the instruction, and it went quite smoothly. run_test.sh rnaseq was s…
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When installing I first get warnings and then an error.
I am also wondering about the python version bcbio uses. Shouldn't it use its own version even during installation, because the log says it uses…
idot updated
10 years ago
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VarScan versions up to 2.3.5 have still bugs that result in improper VCFs being generated (invalid indels, like GA/+A).
For reference: http://sourceforge.net/p/varscan/discussion/1073559/thread/1be8f…
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When restarting a run, bcbio-nextgen's memory usage rises sharply when checking back the results of variant calling (up to ~10 Gb). Since this knocks off one of my cluster machines from the pool the s…
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Pipeline crashes with the following error:
```
[2014-03-17 10:30] multiprocessing: variantcall_sample
Traceback (most recent call last):
File "/cellar/users/mhofree/projects/cancer_ngs/external/ngs…
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The reason is that -o is -O in current bcftools code.
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Despite my cluster having each machine with 24 cores, the latest git master from bcbio-nextgen forces aligners and all other bits to run on 2 cores.
I've set cores for bwa and samtools in the YAML c…
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Howdy! We are checked-out to https://github.com/chapmanb/bcbio-nextgen/commit/e91123c8e68c762c92481ce2ae36aacbaa67eafd version of bcbio and now RNA-seq pipelines are dying on `cutadapt` if I have
``…
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Hello,
I am having 3 multi-sample VCF files (through GATK UnifiedGenotyper, FreeBayes, VarScan); and I am trying to test ensemble variant calling using the following command:
java -Xmx32g -jar bcbio…