convert TCGA hg38 maf to hg 19 maf
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5 months ago
BioNoobie ▴ 10

I tried to use maf2vcf to convert and used the vcf2vcf with remap function, but while doing that in the final file all data is missing (except for #CHROM POS ID REF ALT QUAL FILTER GT:AD:DP ) How do I convert MAF files from TCGA GRCh38 to hg19 without losing the information?

Thanks

TCGA liftover maf mutation • 264 views
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Hello BioNoobie,

why do you want do convert to a reference genome that is outdated for 7 years now?

fin swimmer

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Hi, I am trying to use the tool probabilistic2020 which uses hg19 reference for which I need in hg19

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What about using lifit-over tool? all you need is chromosome-start-end for each variations.

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