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If I delete the DP4 and I use only varscan and somaticniper I have this error:
```
/opt/bcbio.variation.recall/bcbio-variation-recall ensemble -c 4 -n 1 out.fg.gz /home/maurizio/database/hg19_…
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Code:
String outputName = "output";
```
if(args.length >= 3 && !args[2].startsWith("-"))
{
outputName = args[2];
}
```
if using it like that "samtools mpileup -q 1 -f ref…
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Hello!
What for do we have to use [bam-readcount](https://github.com/genome/bam-readcount)? If I am right, varscan already gets this info from input BAMs and stores it in it's VCF!
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I use bcftools 1.6 (but also on 1.8) for concat two varscan results.
I have this error. No variant are present on the ouptut after merging. Here you have the error
```
E::get_intv] Failed to pa…
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Moving this from comment on other issue
> Hi,
>
> I am using bam-readcount (0.7.4) , as part of varscan somatic pipeline, but while applying fpfilter, getting error saying "failed because no readcou…
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I concatenated the germline and LOH variants called by VarScan and used that in cnvkit call. A 43Mb region was called as a deletion with BAF=0. However, by looking at the SNPs that are 0/1 in normal s…
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Hello,
I am using Varscan somatic 2.4.4 to call variants with this command and got an error.
This is the command:
`varscan somatic /path/to/mpileup /path/to/output --mpileup 1 --output-vcf --tu…
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Hi,
I am running Varscan copynumber using the default settings. But met this error message.
Normal Pileup: normal.mpileup
Tumor Pileup: tumor.mpileup
Min coverage: 10
Min avg qual: 15
P-val…
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When running the two snakemake wrappers `Varscan` -> `SnpEff` in succession there is an error thrown https://github.com/pcingola/SnpEff/issues/267#issuecomment-736928876
This does not happen when …
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There is an option that allows large files (like bams) to be streamed from a gs:// address when the tool supports doing so:
https://cromwell.readthedocs.io/en/stable/optimizations/FileLocalization/
…