Question

convert TCGA hg38 maf to hg 19 maf

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3.5 years ago

BioNoobie ▴ 20

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 • 2.5k views

ADD COMMENT • link updated 2.5 years ago by ahadli.farid ▴ 50 • written 3.5 years ago by BioNoobie ▴ 20

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why do you want do convert to a reference genome that is outdated for 7 years now?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

ADD REPLY • link 3.5 years ago by finswimmer 16k

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

ADD REPLY • link 3.5 years ago by BioNoobie ▴ 20

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

ADD REPLY • link 3.5 years ago by Hamid Ghaedi 3.2k

score 1 · Answer 1 · 2021-10-14

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2.5 years ago

ahadli.farid ▴ 50

Hello,

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

Cheers!

ADD COMMENT • link 2.5 years ago by ahadli.farid ▴ 50