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Pipeline crashes on tabix_index function, when running paired variant calling.
trace:
```
[ti_index_core] the file out of order at line 36
' returned non-zero exit status 1
Traceback (most recent ca…
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Excited to try the new bcbio-nexgen just updated yesterday on RNA-seq data. There is a minor issue: In the description of the default RNA-seq pipeline, alientrimmer should be used but I see the curren…
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This is the last command in the log file:
```
[2014-03-06 11:58] java -Xms750m -Xmx2500m -Djava.io.tmpdir=/mnt/tmp/TCGA-CQ-5330/work_norealign/tmp/tmpmmV6dE -jar /cellar/users/mhofree/projects/cancer…
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We've got Gatk and MuTect in non-standard directories and set up correctly in `bcbio_system.yaml`. The correct tools get called, but then weird things start happening, such as bcbio thinking gatk 2.3.…
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I noticed a few problems when including VarScan in calling variants in the NA12878 example. The errors look like this:
```
[2013-11-28 03:31] ukapdlnx118: Genotyping with varscan: ('6', 97599365, 992…
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Hi Brad,
I combined FreeBayes and MuTect in paired variant calling, and the run was fine but only the FreeBayes vcf ended up being copied into the final folder. Any ideas what might be wrong?
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is there a best practice for tumor only analysis? it appears to me that i can only select a tumor-normal paired analysis or the tumor sample will be treated as a normal diploid genome
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VarScan2 has support for copy number variation analysis but I don't think it's supported in bcbio yet, am I correct?
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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…