Question: Aggregate multiple VCFs into a single MAF or generate a multi-sample MAF from a multi-sample VCF
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gravatar for Luca Beltrame
2 days ago by
Luca Beltrame160
IRCCS Istituto di Ricerche Farmacologiche "Mario Negri", Milano, Italy
Luca Beltrame160 wrote:

Note: This is different from the many vcf2maf questions posted around Biostars.

Like many others, I've been in need to generate a MAF file for use in downstream applications like maftools or TRONCO. My final goal is to obtain a multi-sample MAF file like the ones shipped by TCGA.

However, I can't use vcf2maf, because it requires VCFs to only have 2 samples. I have either:

  • Several individual VCFs (1 per sample)
  • One single VCF with information from all samples (with the multiallelic loci decomposed)

The first case would fit vcf2maf, however there is no indication on how to merge multiple MAF files into a single one. And the second one is totally incompatible with vcf2maf due to the use of multiple samples.

The GDC Data Portal docs mention an aggregation workflow which starts from VCFs and ends in MAF, however I've poked around in the GDC sources and I couldn't find anything.

I know this is possible because TCGA does it: but are there any tools to perform this task?

ADD COMMENTlink modified 2 days ago • written 2 days ago by Luca Beltrame160
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