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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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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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Hello,
I am running svtools to add the copynumber information in vcf. CNVnator is up running and I have created hist root file. Genotyping is also done successfully. In the next step where we add c…
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Dear KaBbA authors:
I tried install the package under module load R/4.2.1 by the command:
devtools::install_github('mskilab/JaBbA')
Hit the similar message of
...
The downloaded source pack…
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I generated vcf's from MANTA then annotated them using AnnotSV tool. then tried running vcf2circos tool i get this error :
>> $ vcf2circos --input output.vcf --options Static/options.json --output ou…
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Hi,
I am trying to understand what the columns: `Subclone_CN` and `Subclone_Population` mean in the file `_ratio.txt`.
I have the following examples from the _ratio.txt file
| Chromosome | S…
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Dear All,
I need to ask about an issue with the recent `regexSensitiveDetector`. I am using it on lxplus alma9 machines sourcing the key4hep nightlies. The geometry I am developing has several sens…
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Hi,
I used your pipelines to build a custom annotation file, and found nan in the CNV output, Why did this happen?
Ampliconic_Summary.txt
GeneFamily CopyNumber(MAP=1) CopyNumber(XDG)
…
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Sorry
Long time I am struggling how to provide GISTIC required input like `Num_Probes` and `Segment_Mean`
I have called somatic copy number by `scatngs` and I have copy number output file (attach…
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Thanks for sharing this tool. You mentioned we need to do install_github('aroneklund/copynumber') in order to run GRCh38. My guess is that this is to allow sequenza.extract function to take hg38 assem…