Appropriate genome reference for converting TCGA VCF files to MAF
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3 months ago

I have a directory of MAF files obtained from TCGA and I want to convert it to VCF format. Data source: https://portal.gdc.cancer.gov/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22content%22%3A%7B%22field%22%3A%22cases.project.project_id%22%2C%22value%22%3A%5B%22TCGA-KIRP%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.access%22%2C%22value%22%3A%5B%22open%22%5D%7D%7D%2C%7B%22content%22%3A%7B%22field%22%3A%22files.data_category%22%2C%22value%22%3A%5B%22Simple%20Nucleotide%20Variation%22%5D%7D%2C%22op%22%3A%22in%22%7D%2C%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22files.data_format%22%2C%22value%22%3A%5B%22maf%22%5D%7D%7D%5D%7D&searchTableTab=cases

Reference: GRCh38.d1.vd1 Reference Sequence Source: https://gdc.cancer.gov/about-data/gdc-data-processing/gdc-reference-files

maf2vcf.pl --input-maf maf/* --output-dir VCF -ref-fasta /home/melchua/.vep/homo_sapiens/GRCh38/GRCh38.d1.vd1.fa.tar.gz

Traceback:

Use of uninitialized value $lines in split at /scg/apps/software/vcf2maf/1.6.21/maf2vcf.pl line 107.
ERROR: Make sure that ref-fasta is the same genome build as your MAF: /home/melchua/.vep/homo_sapiens/GRCh38/GRCh38.d1.vd1.fa.tar.gz
maf vcf vcf2maf TCGA • 394 views
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At least you need to tell everyone where you got this " a directory of MAF files obtained from TCGA".

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Thanks for the heads-up. I've added the source of MAF files

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It seems your MAF and reference matches well. So this is not the issue. You might want to check if you have any empty mafs; otherwise, you probably have to read the maf2vcf perl code to figure out what's going on.

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