Question: converting maf to vcf
0
gravatar for ashishchahl
5.8 years ago by
United States
ashishchahl0 wrote:

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

maf2vcf exome • 7.9k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by ashishchahl0
2

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

ADD REPLYlink written 5.8 years ago by Sean Davis26k

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 repectively and each row having different values. So is there any issue with my vcfs file ?


 

ADD REPLYlink modified 5.8 years ago • written 5.8 years ago by ashishchahl0

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.

 

ADD REPLYlink written 5.8 years ago by Sean Davis26k
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