snpEff build Error

Question

[Arup Ghosh]

While building snpEff database for Mitochondrial DNA using Revised Cambridge Reference Sequence genbank(NC_012920.1) file the tool was unable to read protein sequence data and was displaying following error message.

Protein check: NC_012920.1 OK: 0 Not found: 0 Errors: 13 Error percentage: 100.0%

Using the verbose mode I observed the error was caused by the mismatch between SnpEff predicted protein sequence and the Reference protein sequence in genbank file. Has anyone faced a similar issue? Also looking for other alternatives for annotating( to genes & amino acid changes) mitochondrial variants.

[evolozzy]

Were you able to solve this problem? I've tried renaming the chromosome names in gff and fasta files to same name however, ended up having Protein check: mtDNA OK: 0 Not found: 13 Errors: 0 Error percentage: NaN%

[Arup Ghosh]

Check this tutorial: Human mitochondrial DNA annotation in SnpEff