Re: questions about vcf2maf

[Cyriac Kandoth]

Hi Ewa,

Let me CC the cBioPortal team, to make sure I'm not talking rubbish below...

1. Yes, cBioPortal expects a MAF format tab-delimited file, or at least the 4 minimum required columns explained here - https://github.com/cBioPortal/cbioportal/wiki/File-Formats#mutation-data.

2. vcf2maf uses VEP under the hood, which does not report Entrez IDs. It's not a required argument for cBioPortal. Let us know if something breaks (e.g. the protein structure view) and we can show you how to backfill Entrez IDs.

3. Amino_Acid_Change is equivalent to HGVSp_Short, and I believe cBioPortal treats that as a valid alias. If it does not, let us know so we can fix it. As a workaround, you may have to rename the column.

4. Thanks for that bug report. We'll handle it separately as a vcf2maf issue - https://github.com/mskcc/vcf2maf/issues/24 - can you update that issue with a test variant where ALLELE_NUM is not reported?

Cheers!

~Cyriac

On Fri, Oct 23, 2015 at 11:30 AM, Ewa A. Grabowska <egrab...@nygenome.org> wrote:

Hi Cyriac,

I’m a bioinformatics programmer at the New York Genome Center. I have been trying to set up a local version of cbioportal, unfortunately some of the SnpEff/GATK annotations are not really cbio-friendly. Therefore I decided to try out your tool: vcf2maf. Hope you can help me with a few problems that I’ve been having.

1. First of all, my assumption is that the output from vcf2maf should be compatible with cbioportal: is that right?
2. Cbioportal relies on providing Entrez_gene ids, vcf2maf seems to be setting all entrez ids to ‘0’  ($maf_line{Entrez_Gene_Id} = '0’;)
3. Cbioportal takes an AA_change column which seems to be missing in vcf2maf output files.
4. ALLELE_NUM for some reason is not always present in *.vep.vcf file, which causes some downstream problems (precisely this fragment is crashing: 

# Skip effects on other ALT alleles

push( @all_effects, \%effect ) if( $effect{ALLELE_NUM} == $var_allele_idx );)

Thanks so much in advance!

Best,

Ewa Grabowska

Ewa Grabowska | Bioinformatics Programmer
New York Genome Center
101 Avenue of the Americas
New York, NY 10013 
O: (646) 977-7039 | M: (917) 753-6442 
egrab...@nygenome.org

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