for choosing the reference for SNPeff
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7 weeks ago
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When running SNPeff for organisms rather than human, the manual was recommending to search for the reference with the code such as this

java -jar snpEff.jar databases | grep -i equus


and it shows three results.

ASM303372v1.99
EquCab2.75
EquCab3.0.99


when aligning, I used the most recent reference file of nibi which is EquCab3.0 I suppose EquCab3.0.99 is the same reference as EquCab3.0 but I'm not so sure. is there a way I could verify if it's correct?

and does the reference file of databases such as NCBI and Ensembl contain informations for annotation?

In that case are these two files exactly the same?

SNPeff snp reference • 92 views