Issue converting VCF to MAF using snpEff annotations

Question

[Marina Manrique]

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!

[becky3.a]

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.

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

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

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

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

Answer 1

[jimmy_zeng]

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

Answer 2

[mittu1602]

Hi have you installed vep tool well? and to my notice vep needs a particular perl version only. Please verify that too.

Answer 3

[sutturka]

Hi,

Please check the GitHub issues page which have solution for using this tool without installing VEP or use SnpEff annotated files.

Answer 4

[tsy19900929]

https://github.com/tsy19900929/snpeffToMaf