Running vcf2maf on snpeff-annotated vcfs

Question

[becky3.a]

Hi,

I have vcf files that were annotated using snpeff v4.3 and I would like to convert them to maf using vcf2maf.

My first run included the VEP component (below) but I got odd results when I run MutsigCV using the maf file I had generated using vcf2maf:

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 tid --normal-id nid

I then tried another run (below) that skips the VEP annotation step:

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 got the following errors:

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

Where could I be going wrong and how best can I go about this?

Thanks

[Ram]

Please add more relevant tags, like vcf and vcf2maf. software error conveys next to nothing of value, and better tags mean quicker, more targeted responses.

Also, please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[Barry Digby]

To skip the VEP step I read somewhere (probably github) that in the same directory:

cp input.vcf input.vep.vcf

The first step of the script is to annotate using VEP, but if there is already a .vep.vcf file present it skips it.

[Martina]

I read about this possibility to just rewrite name of vcf to *.vep.vcf many times, but the program still wants to anotate the annotated vcf again. Have you got some idea why?

$ vcf2maf.pl --input-vcf input.vep.vcf --output-maf output.vep.maf --vcf-tumor-id input_TUMOR --vcf-normal-id input_NORMAL --tumor-id input_TUMOR normal-id input_NORMAL --buffer-size 100  --ref-fasta  /exports/eddie/scratch/s1959373/external/human_g1k_v37.fasta --filter-vcf 0

Thank you very much :) Martina

Answer 1

[sutturka]

This is a known issue and could happen because of newer annotation types added in SnpEff. Please see the GitHub issues page for vcf2maf.

[becky3.a]

Hi Sutturka, thanks for your feedback. I have been following the vcf2maf GitHub page and issues. I posted an issue with a similar question but I haven't received feedback. Thanks again.

[sutturka]

This issue on github page is very similar and comments on this issue may be helpful.

Answer 2

[becky3.a]

Thanks for your response. I think the only way around this is to forget snpeff and use vep. This becomes a problem for teams that receive and work with vcf files already annotated with snpeff.