Working with SNPEFF for Annotating Variant Calling

Hi all,

Is it possible to run snpEFF on VCF file directly without the database? What is the exactly command line for variant annotation using snpEFF? I am kind of confuse with the command-line I saw on snpEFF webpage http://snpeff.sourceforge.net/SnpEff_manual.html.

Here is the command I used:

java -jar -Xmx29g .../snpEff/snpeff.jar .../reference/HumanTest500k_g1k_H37Rv_decoy.fasta ../fastqs/H37Rv1116.raw.snps.indels.g.vcf > ../H37Rv1116.vcf

Here is my error:

java.lang.RuntimeException: Property: '/usr/people/ajayi/test/enter code hereexample/fastqs/H37Rv_Raw_reads/H37Rv1116.raw.snps.indels.g.vcf.genome' not found at ca.mcgill.mcb.pcingola.interval.Genome.<init>(Genome.java:106) at ca.mcgill.mcb.pcingola.snpEffect.Config.readGenomeConfig(Config.java:619) at ca.mcgill.mcb.pcingola.snpEffect.Config.readConfig(Config.java:587) at ca.mcgill.mcb.pcingola.snpEffect.Config.init(Config.java:434) at ca.mcgill.mcb.pcingola.snpEffect.Config.<init>(Config.java:110) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.loadConfig(SnpEff.java:273) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:955) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.run(SnpEff.java:978) at ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff.main(SnpEff.java:136)

genome snp sequence next-gen software error

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written 10.3 years ago by ajayi •

In case you don't solve your problems with snpEff, I would recommend the VEP tool (variant effect predictor): http://www.ensembl.org/info/docs/tools/vep/index.html It is very versatile and relatively easy to use. For standard genomes (human, etc) is my preferred choice.

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written 10.3 years ago by abascalfederico

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