User: thind.amarinder
thind.amarinder • 20
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Posts by thind.amarinder
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... Thanks for sharing. However, I already did that. Following is the outline of the code
colnames(data2) <- c("Samples","Gene","Impact")
### remove duplicate rows
data <-data[!duplicated(data[,]),]
for(i in 1:nrow(data)) {
for(j in 1:nrow(data)) {
if(i ...
written 7 days ago by
thind.amarinder • 20
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... I am trying, they wrote
If you already annotated a VCF with either VEP or snpEff, you can use those directly:
perl vcf2maf.pl --input-vep test.vep.vcf --output-maf test.maf
perl vcf2maf.pl --input-snpeff test.snpeff.vcf --output-maf test.maf
...
written 7 days ago by
thind.amarinder • 20
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... I got my answer. It is possible with https://github.com/mskcc/vcf2maf/releases/tag/v1.1.0 ...
written 7 days ago by
thind.amarinder • 20
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... not really, I have annotated vcf by VEP. not .vcf ...
written 7 days ago by
thind.amarinder • 20
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... Thanks, cBioportal informed me that I have to make my data public for using the online version. So maybe I should explore, how I can use download and data of other studies in the local version. I am not sure, if it is possible. ...
written 14 days ago by
thind.amarinder • 20
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... Thanks for your valuable reply. I am wondering, using the local cBioportal If, I can use data from other studies available at online version? ...
written 14 days ago by
thind.amarinder • 20
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... It is Mutations and cnv data. I am mainly interested in Oncoprint . ...
written 14 days ago by
thind.amarinder • 20
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... How I can compare my own data with data available in cBioportal and make oncoprint from combined studies.
I don't want to make my data public at the moment. ...
written 14 days ago by
thind.amarinder • 20
• updated
14 days ago by
genomax ♦ 84k
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... I have Vep.vcf files and I would like to convert it into MAF. But I do not want to execute VEP again, as required by vcf2maf.
What are the other possibilities? ...
written 14 days ago by
thind.amarinder • 20
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... @martina I was wondering if you have solved the problem. I have vep.vcf file and want to convert it into MAF. ...
written 16 days ago by
thind.amarinder • 20
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