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,