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!