-
add a script like:
```
preprocess_vcf -v my.platypus.vcf --dp TC > my.dp.platypus.vcf
```
and likewise for varscan and other common options.
-
Hi,
Does these scripts also work when converting copy number findings from VarScan? I see from the other, well-used thread that they work for indels and SNPs at least.
Thanks!
-
I'm getting an error from bioperl that I don't know how to solve. I assume something with my `bioperl` is broken as this code works on a colleagues ComputeCanada account.
```
[moldach@cedar1 SNA…
-
Old internal issue:
https://jira.gsc.wustl.edu/browse/CI-77
-
Hi,
I am intending to use cmvdrg software for detecting possible resistance variants in a CMV VCF file. However, it seems like my VCF file input is not valid for cmvdrg. This is the error message i…
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Dear Sir,
I am very impressed by the author's work and the depth of the analysis in your article. Also, I would like to thank you for sharing the scripts.
However, I just started using your Fixed_S…
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Hi!
I would like to know if it is possible to use Smurf with tumor-only mode.
I know VarScan and Strelka2 can`t work with tumor-only, so I would have only the VCFs for freebayes, GATK and VarDict. I…
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If you check it against the the 2.4.4 source, the only difference is the internal file name.
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Use case: variant callers that insert fixed sample names like VarScan, or the TCGA data, which uses NORMAL/TUMOR as sample names.
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I'm trying to filter a snp file using the command
```
java -jar ~/VarScan.v2.3.9.jar filter VariantsCalling/1.varScan.snp –-indel-file VariantsCalling/1.varScan.indel –-output-file VariantsCalli…