Converting a multi-sample single VCF to MAF
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10 weeks ago
Vanish007 ▴ 40


I have a single vcf file with more than 3,000 samples. Due to its size (over 3TB unzipped), I have also split it by chromosomes and zipped them. Is there a memory efficient way to convert a multi-sample VCF file to MAF and retain the sample information for downstream analysis? I have a limit to our HPC storage to 5TB so it will stop any running scripts if memory goes above 5TB.

I saw from previous posts that tools like vcf2maf are not compatible with multi-sample vcfs, but since most of the posts were older, I wanted to know if there have been any updated tools or strategies for vcf to maf conversion, especially when dealing with thousands of samples.

Thanks for the help!

vcf maf vcf2maf maftools • 122 views

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