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Hi,
I tried the install bcbio with the command below.
```
python bcbio_nextgen_install.py /usr/local/share/bcbio --tooldir=/usr/local --genomes GRCh37
```
My bcbio installation stuck at the step …
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I'm seeing the error:
Batch SA730 requires both tumor and normal BAM files for VarScan cancer calling
I have all my libraries listed as tumor (they are cell lines).
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Somewhere along the lines, the fileDate and reference headers were removed from your galaxy tool. With these fields missing, the dcc_validator throws an error.
I have a local branch for the vcfProces…
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Hi,
I added structural variant detection to the tumor/normal pipeline and then run initially with n=10,
here is the output below but run with n=1, any suggestions about how to improve the debugging of…
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Hello,
I am trying to install Bc-Bio on a linux cluster, but keep running into this issue:
```
The following packages will be UPDATED:
singledispatch: 3.4.0.3-py27_0 --> 3.4.0.3-…
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Looks like vcf support has been added to Scalpel recently: http://sourceforge.net/p/scalpel/code/ci/master/tree/
Opening this ticket while I'm looking into testing Scalpel and integrating it within b…
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Hi,
I have finished the tumor-normal paired cancer variant calling pipeline and found final vcf files for somatic mutations in "final" folder. However, currently, I also intend to get the germline var…
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Hi Brad,
Recently, I used:
bcbio_nextgen.py upgrade -u development --data --tools
to update bcbio_nextgen
However, an error was occurred for pkg-config-0.28.tar.gz, the info was:
```
[localhost] …
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Samtools
PicardTools
MuTect
SomaticSniper
VarScan
Pindel
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Hi
I am not sure what the difference between the two fields `MQ` and `QUAL` is in the vcf output of VarDict as the explanations are very similar:
```
##FORMAT=
##FORMAT=
```
If the QUAL does not re…