-
```
If you label a lane as "illumina" when it is really "sanger", the
copy_uncompress fastq step can sometimes not see the fastqc log file that
automatically checks the quality encoding. This resul…
-
hi, i was running Cancer tumor normal.
there is my log files:
[bcbio-nextgen-commands.log](http://7xpt71.com1.z0.glb.clouddn.com/bcbio-nextgen-commands.log)
[bcbio-nextgen.log](http://7xpt71.com1.z0.…
-
Hi,
I am getting an error about mutect config file is not found. However, I dont have a screen shot neither there is not an evidence related with this problem in the log files. I followed all the ste…
-
Hi,
I would like to reproduce Tumor paired variant calling for better understanding bcbio. I am trying to operate this task on AWS EC2 machines however I am interfering with problems.
First;
I belie…
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Hi,
I am trying to validate if bcbio is set right in our HPC. For this, we need a small data that can be optimised easily. That is why I would like to reproduce chr 6 data. When I run the process, th…
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Dear Brad;
I tried running final template on bam files. Actually I think it did pretty well. However, during the ensemble phase I got an error and pipe got broken. I believe this problem might be rel…
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bam object should be another element in files array with type BAM ; mucor should ignore all type BAM
{
"bam": [
{
"path": "project/dir1/sample1.bam"
}
],
"…
-
Hi, just a simple question: is it only mutect that supports tumor variant calling without normals? Principally, should not varscan, freebayes and perhaps also other tools be able to do this?
-
Hi,
I am really confused the fact that my run gets failed. I ran exactly two configuration files(the only change was the path's of the files), one in bcbio_nextgen, one in bcbio-vm. and I got interru…
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Hi again,
I would like to include indel calling to the process, there fore I added pinned to the timor-normal paired cancer tutorial. However, it freezes during execution with out error without any w…