Basic SNPeff Tutorial (using custom database)

Basic tutorial for making a custom database and annotate a VCF file. using SNPEff. This example was made for an REU student from my lab using the UGA sapelo2 cluster environment.
For more information: rpbaptista.wee...
SNPEff manual available: snpeff.sourcefo...

[@maisapinheiro4358]

This video has so many levels of joy for people just starting with VCF filtering.

[@advdheiden]

This was extremely helpful! Thank you very much for making this.

[@sushantadeb2469]

Your tutorial makes my work super easy thanks a lot.

[@callierodgerschappell5868]

This is an awesome, really helpful tutorial. Thank you for making it!

[@cameronjack1095]

This is gold. Thank you very much!

[@prashantkathait4528]

You saved my day!!! Thanks for the tutorial.

[@palesa1623]

Well explained. Thank you so much for this !

[@nnzhou9493]

Thank you!

[@amruthaas3846]

Hi. Great tutorial. can you tell me how to use a different codon table for the new database?

[@arigatooo24]

Could you please tell how did you add ids to your vcf file in a new column ? eg. CPATCC_0036010 ?

[@swatishrestha2855]

Great video. Its strange that snpeff showed error while building the database when the .fa and .gff files names were other than sequences.fa and genes.gff. But when I changed the names then everything worked fine. Just curious why this happened? Any idea?

[@cameronjack1095]

There are two import processes. If you are using the method showed here (directory with the genome name, in this case cpar_ATCC) then you need to use the specified file names. I.e. sequences.fa and genes.gtf.

when looking at snpeff annotation many times there are different entries for the same position. When annotating genes. how do you chose in between them ?

[@Dihgo]

use SNPsift to generate the table with the feature information and for the featureID use the index 0 (example: "ANN[0].FEATUREID". It will do the cleaning trick =)