6
votes
Tools to do VCF to MAF and MAF to VCF conversion?
You can use annovar to annotate the vcf, then convert it to maf using the function annovarToMaf of maftools bioconductor package.
- 333
5
votes
Accepted
3
votes
Accepted
Merging matched parts of two dataframes
If you have issue with memory and dealing with large object, maybe data.table is the way to go (https://github.com/Rdatatable/data.table/wiki):
Let's take two ...
- 1,021
1
vote
Accepted
Problems when using vcf2maf
Install it via Anaconda/conda.
conda install -c bioconda vcf2maf
conda install -c bioconda/label/cf201901 vcf2maf
I personally like Anaconda-navigator for OSX but ...
M__♦
- 11.9k
1
vote
Accepted
Error in installing vcf2maf
Install it via anaconda/conda either,
conda install -c bioconda vcf2maf
conda install -c bioconda/label/cf201901 vcf2maf
I would be surprised if that installation ...
M__♦
- 11.9k
1
vote
Merging matched parts of two dataframes
Read the manuals for data.table::merge and base::merge.
This (wrong syntax):
...
- 1,042
1
vote
GMAJ error: Exception in thread "main" java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
It's a programming error that should look like this:
StringBuffer sb = (...)
(...)
String s = (String)sb;
while it should be
...
- 1,501
1
vote
Accepted
Downloading an open-source MAF with tumor and normal BAMs?
There's the NCI Genomic Data Commons:
For all submitted sequence data, including BAM alignment files, the GDC generates new alignments in BAM format using the latest human reference genome GRCh38 ...
- 13.8k
Only top scored, non community-wiki answers of a minimum length are eligible