converting maf to vcf

Question

[ashishchahl]

Hi,

I am working on exome data from tcga. I downloaded it in .maf format and want to convert it in .vcf format using maf2vcf.pl (https://github.com/ckandoth/vcf2maf/blob/master/maf2vcf.pl) script and I found warning as described below.

ashish@ashish-HP-Pavilion-15-Notebook-PC[scripts] perl maf2vcf.pl --input-maf /home/ashish/project/Somatic_Mutations/BI__IlluminaGA_DNASeq_curated/Level_2/broad.mit.edu__IlluminaGA_curated_DNA_sequencing_level2.maf --output-dir GRCh38
WARNING: Skipping variant at 4:100265826. Failed to fetch bps from reference FASTA!
WARNING: Skipping variant at 2:89082219. Failed to fetch bps from reference FASTA!
WARNING: Skipping variant at 2:89083945. Failed to fetch bps from reference FASTA!

In maf2vcf.pl script I edit the path of reference genome GRCh38.

I use GRCh38 instead of GRCh37.

And I still get Warning.

Help me out,

Thanks

[Sean Davis]

Do the chromosome names in your FASTA file match those in the maf file?

[ashishchahl]

FASTA file has chromosome name "chr" and maf file has chromosome name numeric. So I change the maf file chromosome name to "chr". Then I run the command and not getting any warning and I got my vcf files too.

In my vcf file, in tumor and normal columns I get 0/1:.,.:. and 0/0:.,.:. respectively in each row of these columns while in vcf2maf master, in test.vcf tumor and normal columns have 0/1:10,10:20 and 0/1:30,5:35 respectively and each row having different values. So is there any issue with my vcfs file?

[Sean Davis]

Well, it sounds like your problem is fixed. As to whether or not your VCF file is "correct", that will be up to you to decide. Clearly, there are some missing values represented by '.', but that may not be a problem, depending on your use case for the VCF file.