SnpEff Query

Question

[ramshahaya]

Hi Biostars community,

I would like to request you to help me regarding this. I have performed GATK analysis using GATK haplotype caller. Then I have been trying to annotate VCF file obtained using GATK pipeline. I have used snpeff tool to annotate the vcf file.

First I had download already available database using given below commands. java -jar /home/anaconda3/share/snpeff-5.0-1/snpEff. databases | grep -i "bos taurus"

Then I ran given below commads.

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar snpEff_v5_0_UMD3.1.75 2K_chr22.vcf.gz > 2K_chr22_annotation.vcf.gz java.lang.RuntimeException: Property: 'snpEff_v5_0_UMD3.1.75.genome' not found at org.snpeff.interval.Genome.<init>(Genome.java:104) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:693) at org.snpeff.snpEffect.Config.readConfig(Config.java:661) at org.snpeff.snpEffect.Config.init(Config.java:487) at org.snpeff.snpEffect.Config.<init>(Config.java:121) at org.snpeff.SnpEff.loadConfig(SnpEff.java:449) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:939) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:923) at org.snpeff.SnpEff.run(SnpEff.java:1188) at org.snpeff.SnpEff.main(SnpEff.java:168)

Kindly suggest me. It would be really appreciable. Thank you so much in advacne

[cpad0112]

java -jar /home/anaconda3/share/snpeff-5.0-1/snpEff databases | grep -i "bos taurus"

This doesn't download databases

Your command is incorrect. It should be:

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar UMD3.1.75 snpEff_v5_0_UMD3.1.75 2K_chr22.vcf.gz > 2K_chr22_annotation.vcf.gz

if you haven't downloaded UMD database, download it first:

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar download -c /home/anaconda3/share/snpeff-5.0-1/snpEff.config -v UMD3.1.75

[ramshahaya]

Dear User,

Thank you so much.

I am able to run this program using given below command without using snpEff_v5_0_UMD3.1.75 suggested by you in your previous answer.

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar UMD3.1.75 snps.vcf > snps_annotation.vcf

I have another query regarding your previous answer of my query. I would like to know about this (snpEff_v5_0_UMD3.1.75) in the given below command. what is the meaning of this and why you have used it as you have suggested me. Beacuse If I use this, then I get error. Without this there is no error.

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar UMD3.1.75 snpEff_v5_0_UMD3.1.75 2K_chr22.vcf.gz > 2K_chr22_annotation.vcf.gz

Would be grateful. Thank you so much in advance.

[cpad0112]

From your post, i assumed that snpEff_v5_0_UMD3.1.75 2K_chr22.vcf.gz is your file name from this line java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar snpEff_v5_0_UMD3.1.75 2K_chr22.vcf.gz > 2K_chr22_annotation.vcf.gz. I should have mentioned it this way:

java -Xmx4g -jar /home/anaconda3/share/snpeff-5.0-1/snpEff.jar UMD3.1.75 input.vcf.gz >  output.vcf.gz

In OP, you were using a database name, that weren't there in SNPeff database. Now that you are using correct version (i.e UMD3.1.75 in place of snpEff_v5_0_UMD3.1.75), your function is successful.

[ramshahaya]

Thank you so much :)