Is it possible to generate a single maf file from multiple vcf files using vcf2maf ?

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5.4 years ago

sselvar ▴ 40

Hi,

I have 40 raw vcf files and I was able to convert all these 40 vcf files to 40 individual maf files. But, when I read the GDC pipeline it was mentioned that a single maf files could be generated for a single project involving multiple vcf files. I was curious to know if vcf2maf can do this conversion i.e., if vcf2maf can convert multiple vcf files to a single aggregated maf file. If it can be done, can you tell how to do so?

genome sequencing SNP • 1.7k views

ADD COMMENT • link updated 5.4 years ago by finswimmer 16k • written 5.4 years ago by sselvar ▴ 40

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Why not just apply vcf2maf to individual file and then merge all the maf with sample id index?

ADD REPLY • link 5.4 years ago by Shicheng Guo ★ 9.6k

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Yeah, I can do that as well but just wanted to know if the tool can itself generate a single maf file. Thank you for the quick reply!

ADD REPLY • link 5.4 years ago by sselvar ▴ 40

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