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mskcc / vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
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VCF2MAF and allele frequency #344

Open jmf432x opened 1 year ago

jmf432x commented 1 year ago

I am converting a VCF to MAF using the VCF2MAF program, and importing that into cbioportal. I notice that the "af" from the INFO field is not making to the MAF output file.

Snippet from VCF: (the "af" value is no where to be found in maf file)

INFO=

CHROM POS ID REF ALT QUAL FILTER INFO

chr17 27419372 . C A . PASS af=0.31410256;cds_syntax=5176G>T;cosmic_status=UNKNOWN;depth=468;effect=MISSENSE;gene_name=MYO18A;protein_syntax=A1726S;transcript_name=NM_078471

Perl VCF2MAF command: perl vcf2maf.pl --input-vcf /home/jmf432/test_vcf_files/ORD-1543927-02.vcf --output-maf /home/jmf432/test_vcf_files/ORD-1543927-02-JF2.maf --ref-fasta /home/jmf432/.vep/homo_sapiens/109_GRCh38/Homo_sapiens.GRCh38.dna.toplevel.fa.gz --vep-path /home/jmf432/vep/ensembl-vep-release-109.3 --ncbi-build GRCh37 --verbose --vep-overwrite --any-allele --retain-info af

Snippet from the output MAF file (all the af fields are blank):

DOMAINS AF AFR_AF AMR_AF ASN_AF EAS_AF EUR_AF SAS_AF AA_AF EA_AF

I was expecting to see the "af" value from the VCF file in the MAF output file, but it is not.

Can someone please explain why and correct me if I have a misunderstanding ?****

jmf432x commented 1 year ago

anyone?

tanghaibao commented 1 year ago

In my VCF, the AF field is in the FORMAT column, so I could get VAF with --retain-fmt AF instead of --retain-info. Then the VAF column is t_AF in the resulting MAF.

berguner commented 9 months ago

@tanghaibao AF in the FORMAT column represents the allelic fraction which is the fraction of reads supporting the variant in that sample. @jmf432x is asking about population allele frequency of the variant seen in the population databases like GnomAD or dbSNP.

Back to the original issue, I am also missing GnomAD AF in my MAF file. Would be interested if anyone has figured out the issue and a solution.

grantn5 commented 8 months ago

Hi @berguner I have been using the

Nextflow pipeline here (dev branch)

https://github.com/FriederikeHanssen/vcftomaf/tree/dev

To do the conversion it automatically includes all VEP annotations present in the info column