Working with SNPEFF for Annotating Variant Calling

Question

[ajayi]

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)

[abascalfederico]

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.