SnpEff Error

Question

[bestone]

Hello guys, I. run this code : snpEff Prunus_armeniaca_cv_Stella.gff3.gz output.vcf > output.txt

I am getting this Error! Could you pls help me with this issue?

java.lang.RuntimeException: Property: 'Prunus_armeniaca_cv_Stella.gff3.gz.genome' not found at org.snpeff.interval.Genome.<init>(Genome.java:104) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:784) at org.snpeff.snpEffect.Config.readConfig(Config.java:751) at org.snpeff.snpEffect.Config.init(Config.java:529) at org.snpeff.snpEffect.Config.<init>(Config.java:116) at org.snpeff.SnpEff.loadConfig(SnpEff.java:429) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875) at org.snpeff.SnpEff.run(SnpEff.java:1141) at org.snpeff.SnpEff.main(SnpEff.java:160)

Answer 1

[Pierre Lindenbaum]

As far as I know,, this is not how SNPEFF works; You must first create a database with gff3 : https://pcingola.github.io/SnpEff/se_buildingdb/

A straightforward solution would be to use bcftools csq -l -f ref.fa -g in.gff3 in.vcf