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my row output from ANNOVAR is below.
```
Chr Start End Ref Alt Func.ensGene Gene.ensGene GeneDetail.ensGene ExonicFunc.ensGene AAChange.ensGene Otherinfo
…
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Hello,
Sorry, I am being stopped when running oncoplot
```
> oncoplot(maf = laml, top = 1, fontSize = 12)
Error in oncoplot(maf = laml, top = 1, fontSize = 12) :
Cannot create oncoplot for…
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Hello,
MANTA2 seems like a very convenient tool! It performed very quickly for a quick test analysis that I ran!
I am interested in using MANTA2 for analyses that are mostly brain development re…
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Hi,
I have annovar format files and would like to convert them to maf format. I'm having trouble converting them. It says Tumor_Sample_Barcode not found, though I have added it in my file.
Here is …
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really keen to get this working but when i follow the documentation get an error loading data
root@debian-template:~/GenESysV# python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz…
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Hello,
I'm trying to import a small [VCF](https://github.com/vatlab/VariantTools/files/2479881/test.vcf.gz), but I see vtools discards some variants. Why does he do it ?
` bcftools view -H -c1 .…
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It seems Annovar uses the previous Gene.refGene to annotate a variant of the next gene. For example, NM_152486 is for SAMD11 but in the third line it is still in the Gene.refGene field where NM_015658…
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I manually maf file from raw VCF, vep annotated VCF and annovar results.
```
Tumor_Sample_Barcode | Chromosome | Start_Position | End_Position | Reference_Allele | Tumor_Seq_Allele2 | Hugo_Sym…
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Hi All,
I tried to use maftools to do genetic analysis. However, no matter which function I try to use. they always report errors like the following:
> getSampleSummary(laml)
unable to fi…
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Hi, I went to http://annovar.openbioinformatics.org/en/latest/user-guide/download/ and clicked can be download here, and there's no response what so ever. Could you please check what the problem might…