convert TCGA hg38 maf to hg 19 maf
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
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ahadli.farid •
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BioNoobie •
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BioNoobie •
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Hello,
Do not know if it is still relevant but CrossMap have a utility called CrossMap.py maf for this exact purpose.
Cheers!
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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why do you want do convert to a reference genome that is outdated for 7 years now?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
Hi, I am trying to use the tool probabilistic2020 which uses hg19 reference for which I need in hg19
What about using lifit-over tool? all you need is chromosome-start-end for each variations.