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Hi Brad;
I believe I am one step away for the implementing scalpel + variants callers to the Icgc Data. I am gonna do this !! :) .On my latest run, I tried to include pindel and scalpel (on separate …
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Hi,
I am using bcbio to call variant for my paired timor-normal cancer patient samples. My data comes from ICGC consortium as mapped & aligned bam files.
Briefly, bcbio uses for callers to call var…
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Hi,I get a problem when I use vcf2maf perl script, and I don't know how to solve it.Can you help me?Thanks!
ERROR: --regulatory is not available for this species at /home/xiaxy/vep/variant_effect_pre…
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It seems to me that pileup command is using VARSCAN_THREADS whereas PILEUP_THREADS are requested from the scheduler. (illumina_somaticVariants.pm)
hinri updated
8 years ago
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Running bcbio-nextgen locally in parallel:
```
bcbio_nextgen.py ../config/CX5461_yeast.yaml -t local -n 50 --retries 3
```
I receive the following errors related to VarScan:
```
[2015-12-10T03:06Z]…
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Hi Cyriac,
with the previous version of vcf2maf I had no problem annotating hg19 vcf even with vep 82, but with the current 1.6.3 I am getting this error... I was trying to figure out if zoo make some…
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Template command on the yaml file with qsignature duplicates the entry in the alignment section and the top level of the sample yaml
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Hi, is there any reason why the PileUp format is not included in this repo? Does there exist any up-to-date specification? I found only http://samtools.sourceforge.net/pileup.shtml but it is marked as…
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Hi I am running varscan in tumor only mode and i get this error. if I run the outside bcbio it return no error and it return
I have upload the partial bam in this folder
https://drive.google.com/op…
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Hi,
I have been running the process below for almost 3 days. It went without a problem until this step. I did not change anythin in the configuration related to mutation calling but I dont know why d…