Error while running vcf2maf utility

Question

[mkaushal]

Hello,

I have vcfs from Varscan (somatic mode) and I am trying to convert them to maf using the tool vcf2maf : https://github.com/ckandoth/vcf2maf. I didn't face any issues with the snp vcf. But with some of my indel vcfs I am encountering the following error:

ERROR: Unrecognized effect "intragenic_variant". Please update your hashes! at ~/vcf2maf-master/vcf2maf.pl line 599, <GEN1> line 815.
Attempt to free unreferenced scalar: SV 0x1dd85c0, Perl interpreter: 0x1755010 at ~/vcf2maf-master/vcf2maf.pl line 599, <GEN1> line 815.

Can someone please help me understand the error. The snp.vcfs also had "intragenic_variant" as an effect and it ran fine. Is this some issue related to memory?

Regards,
Madhurima

Answer 1

[Cyriac Kandoth]

vcf2maf returns an Unrecognized effect error when the variant's effect (aka consequence) is not handled in this prioritization table. When you see this error, it's best to open a new issue on Github, so I can figure out how to prioritize this effect type. But posting it on Biostars is fine too, as long as you use the vcf2maf keyword, which you did... thanks! So the term intragenic_variant was not being handled earlier, but it is now. Please fetch the latest master branch of vcf2maf, and try again.

[mkaushal]

Hi Cyriac,

Thanks a lot for your help. The script works fine for me now. I have another question regarding the maf file that was generated. The Entrez id value for all genes is "0". Is there a reason for this? Can I solve this because I need Entrez ids for downstream analysis. Please let me know.

~Madhurima

[Cyriac Kandoth]

Always better to open a new thread for unrelated questions, to make it easier for folks to find it. But yea, vcf2maf doesn't report Entrez IDs. For a given gene name, you can retrieve them from Entrez E-utils, but often need to be disambiguated.