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?