Obtain variant allele fraction from VCF

[bioinfo-dirty-jobs]

I run the ~last~ latest version of vcf2maf on my data. I want to obtain ~vcf~ VAF comparable to data from TCGA. I could not find VAF in the maf file of variants from tumor and normal "vcf2maf.pl --input-vcf {input} --output-maf {output} --vep-path {params.db_ens} -ref-fasta {params.fst} --tumor-id {params.tumor_id} --normal-id NORMAL

[ckandoth]

Your goal is confusing. What is the input format you have? And what is the output format you want?

[bioinfo-dirty-jobs]

@ckandoth I use as input vcf from mutect2 and varscan 2.4. I would like to obtain the variant allele frequency like what we obtain in the maf file of tcga.

[ckandoth]

ok thanks. In a standard VCF, the read counts and REF/ALT allele counts are usually in columns named after sample IDs. If you specify the correct sample IDs using arguments --tumor-id and --normal-id, then vcf2maf will try to retrieve read/allele counts from under those columns. However, in VarScan VCFs, the columns are always named TUMOR and NORMAL. For this reason, vcf2maf allows you to separately specify --vcf-tumor-id and --vcf-normal-id to indicate the column names used in the input VCF, in case they are different from your actual sample IDs.

You can read much more about all this in the documentation - https://github.com/mskcc/vcf2maf/blob/v1.6.16/README.md#quick-start

[slzhao]

Hello, Do you have any follow up for this? If I understand the question correctly, it is a request for variant allele frequency (VAF) in each sample, usually under AF or FA tag in vcf file. This is important in some analysis. May I know if you are planning to provide this option?

Thanks! Shilin