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Tutorial: Human mitochondrial DNA annotation in SnpEff

1) First create a directory in the snpEff data folder called NC_012920.

2) Download the complete Genbank record (select GenBank full option) of NC_012920 from NCBI and save it in data/NC_012920 folder. Rename the downloaded file to genes.gbk.

3) From the same page download the complete protein sequence using Coding Sequences option then select FASTA protein and rename the file to protein.fa.

4) Add the following record in snpEff.config file.

NC_012920.genome : NC_012920
        NC_012920.chromosomes : NC_012920.1
        NC_012920.NC_012920.1.codonTable : Vertebrate_Mitochondrial

5) Now build annotation database using the following command;

java -jar snpEff.jar build -d NC_012920
chrmt snp snpeff
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updated by Ram Ram • written by Arup Ghosh Arup Ghosh

What should I download exactly in step 2) from NCBI? Also, I don't see a Coding Sequences option.

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written by user_without_id user_without_id

Click on Send to option on the top right corner of the page.

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written by Arup Ghosh Arup Ghosh

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