Issue converting VCF to MAF using snpEff annotations

Hi there!

I'm trying to convert my VCF to MAF using snpEff for the annotations but I'm getting these errors (I'm copying just a set of them but I'm getting the same errors for every variant called in the VCF)

Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 772, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 773, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 774, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 775, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 776, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 777, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 778, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 779, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 780, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 781, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 782, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 783, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 784, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 785, <GEN1> line 2259.
Use of uninitialized value $effect in pattern match (m//) at vcf2maf.pl line 786, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 787, <GEN1> line 2259.
Use of uninitialized value $effect in string eq at vcf2maf.pl line 788, <GEN1> line 2259.

I'm using this script vcf2maf and this command

perl vcf2maf.pl \
  --input-vcf MMB34.vcf \
  --output-maf MMB34.maf \
  --snpeff-path /home/ec2-user/snpEff \
  --snpeff-data /home/ec2-user/snpEff/data \
  --use-snpeff \
  --ref-fasta /media/ephemeral0/.vep/homo_sapiens/76_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa

Any ideas of what I'm doing wrong?

Thanks!

vcf vcf2maf snpeff maf

• 7,920 views • link

updated 4.3 years ago by Ram

• written 11.5 years ago by Marina Manrique

Hi,

Kindly share how to got around this. I have vcf files that were annotated using snpeff and I would like to convert them to maf using vcf2maf.

I used:

"perl vcf2maf.pl --input-vcf file.vcf --output-maf file.maf --ref-fasta ~/GRCh37-lite.fa --species homo_sapiens --tumor-id ddd --normal-id dddnn"

I get the following errors:

Use of uninitialized value in list assignment at ~/vcf2maf.pl line 649, <gen4> line 2186.

My initial run included VEP (below) but I got wrong results when I run MutsigCV using the maf file I had generated:

"perl vcf2maf.pl --input-vcf file.vcf --output-maf file.maf --ref-fasta ~/GRCh37-lite.fa --vep-forks 4 --vep-path ~/vep --ref-fasta $VEP_DATA/homo_sapiens/86_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz --species homo_sapiens --tumor-id ddd --normal-id dddnn"

Where am I going wrong?

Thanks

• 1 views • link

written 8.1 years ago by becky3.a •

4 answers

I don't think this tool can hold on the vcf files from snpEFF, as below:

perl vcf2maf.pl  --help
Usage:
     perl vcf2maf.pl --help
     perl vcf2maf.pl --input-vcf WD4086.vcf --output-maf WD4086.maf --tumor-id WD4086 --normal-id NB4086

Options:
     --input-vcf      Path to input file in VCF format
     --output-maf     Path to output MAF file
     --tmp-dir        Folder to retain intermediate VCFs after runtime [Default: Folder containing input VCF]
     --tumor-id       Tumor_Sample_Barcode to report in the MAF [TUMOR]
     --normal-id      Matched_Norm_Sample_Barcode to report in the MAF [NORMAL]
     --vcf-tumor-id   Tumor sample ID used in VCF's genotype columns [--tumor-id]
     --vcf-normal-id  Matched normal ID used in VCF's genotype columns [--normal-id]
     --custom-enst    List of custom ENST IDs that override canonical selection
     --vep-path       Folder containing the vep script [~/vep]
     --vep-data       VEP's base cache/plugin directory [~/.vep]
     --vep-forks      Number of forked processes to use when running VEP [4]
     --buffer-size    Number of variants VEP loads at a time; Reduce this for low memory systems [5000]
     --any-allele     When reporting co-located variants, allow mismatched variant alleles too
     --ref-fasta      Reference FASTA file [~/.vep/homo_sapiens/91_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz]
     --filter-vcf     A VCF for FILTER tag common_variant. Set to 0 to disable [~/.vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz]
     --max-filter-ac  Use tag common_variant if the filter-vcf reports a subpopulation AC higher than this [10]
     --species        Ensembl-friendly name of species (e.g. mus_musculus for mouse) [homo_sapiens]
     --ncbi-build     NCBI reference assembly of variants MAF (e.g. GRCm38 for mouse) [GRCh37]
     --cache-version  Version of offline cache to use with VEP (e.g. 75, 84, 91) [Default: Installed version]
     --maf-center     Variant calling center to report in MAF [.]
     --retain-info    Comma-delimited names of INFO fields to retain as extra columns in MAF []
     --min-hom-vaf    If GT undefined in VCF, minimum allele fraction to call a variant homozygous [0.7]
     --remap-chain    Chain file to remap variants to a different assembly before running VEP
     --help           Print a brief help message and quit
     --man            Print the detailed manual

• 1 views • link

written 8.3 years ago by jimmy_zeng