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When running a calling command like `mpileup2cns` without specifying the `--p-value` argument, VarScan outputs
> Warning: No p-value threshold provided, so p-values will not be calculated
It appear…
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There should be new datatypes for somaticsniper, muse, and varscan maf files.
The following commands:
gdc_mirror --config tcgaSmoketest.cfg
gdc_dice --config tcgaSmoketest.cfg
yield the fo…
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When subsets of the callers make a variant call, we get a nice dash-delimited list of the outputs in the "set" attribute: `set=mutect-varscan-strelka`
When every caller makes a call, we just get `…
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I see for CRISPREessoWGS you need to specify an interval in which the analysis is run on. I'm wondering if CRISPresso can be run on the entire genome (entire WGS data)?
Thanks!
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As the picture show, the sample have snv and indel so close. but the varscan's somatic( …
welyt updated
8 years ago
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Hey Nick,
This is the farthest I've got, running your pipeline on the server using the HUM samples to try. I've cloned the pipeline in my personal space, I see I also have it in the .nextflow direc…
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Hello!
If there is no "prefix" in workflow.step.run.inputBinding:
```
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/cwltool/workflow.py", line 587, in job
…
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I ran VarScan2 on my paired pileup files, and I do not think there are problems with the input files (please see attached a part of the input files), but I really do not understand why it gave me outp…
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Dear Martin (Page),
I have tried the Galaxy Flavor Generator (using
http://bit.ly/galaxy-flavor-generator)
I have selected only a few programs (see Dockerfile at the end of my
email). When I try to …
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HI Varscan developper,
In order to use the false positive filter, i will need to run the bam-read-count on the called mutations, I know I can generate the positions for the snp for bam-read-count, …