comparison snpEff_macros.xml @ 15:479c4f2f4826 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit 999eca8a05f17ae567f99b8ca3394f2105491173

14:85ca751407c3

**Create your own database**

In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:

 #. Download Genbank record corresponding to your genome of interest from NCBI.
 #. Use **SnpEff build** to create the database.
 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).

Creating custom database has one benefit. The **SnpEff build** tool normally produces two outputs: (1) a SnpEff database and (2) FASTA file containing sequences from the Genbank file. If you are performing your experiment from the beginning by mapping reads against a genome and finding variants before annotating them with SnpEff you can use **this FASTA file** as a reference to map your reads against. This will guarantee that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.

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15:479c4f2f4826

**Create your own database**

In cases when you are dealing with bacterial or viral (or, frankly, any other) genomes it may be easier to create database yourself. For this you need:

 #. Download Genbank record corresponding to your genome of interest from NCBI or use annotations in GFF format accompanied by the corresponding genome in FASTA format.
 #. Use **SnpEff build** to create the database.
 #. Use the database in **SnpEff eff** (using *Custom* option for **Genome source** parameter).

Creating custom database has one major advantage. It guaranteess that you will not have any issues related to reference sequence naming -- the most common source of SnpEff errors.

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