convert TCGA hg38 maf to hg 19 maf

Question

[BioNoobie]

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

[finswimmer]

Hello BioNoobie,

why do you want do convert to a reference genome that is outdated for 7 years now?

fin swimmer

[BioNoobie]

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

[Hamid Ghaedi]

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

Answer 1

[ahadli.farid]

Hello,

Do not know if it is still relevant but CrossMap have a utility called CrossMap.py maf for this exact purpose.

Cheers!