Identification of SNP effect on amino acid. Issue with SnpEff

Question

[valerie]

Hi guys,

I have a list of SNPs for my 8 mouse samples in a single 3GB vcf file. I want to identify those SNPs that lead to amino acid change in proteins (get information on whether my mutation is silent, missence or nonsence for each of the samples). I tried SnpEff for that, but got an error:

java -Xmx4g -jar snpEff/snpEff.jar -v -stats ex1.html mm10 mice_output_snp.vcf > mice_output_snp.ann.vcf

00:00:00.000 SnpEff version SnpEff 4.1c (build 2015-03-29), by Pablo Cingolani 00:00:00.031 Command: 'ann' 00:00:00.054 Reading configuration file 'snpEff.config'. Genome: 'mm10' java.lang.RuntimeException: Property: 'mm10.genome' not found

I've tried to use GRCm38 and GRCm38.81 instead mm10, but this didn't help. Could someone help me with SnpEff please or suggest any other tool for my problem?

Thank you in advance!

[WouterDeCoster]

Alternatives for SnpEff are VEP and Annovar, but I would expect you should get SnpEff to work for a commonly studied organism such as mouse.

[valerie]

As far as I understand VEP is an online tool where you have to upload a file, and I have this huge file on my server. I will look at Annovar, thanks!

[WouterDeCoster]

You can also use VEP locally.

[Pierre Lindenbaum]

did you install the database mm10 with "snpeff download" ?

[valerie]

Yes, I've tried doing that in several ways: java -Xmx4g -jar /opt/software/snpEff/snpEff.jar download -v mm10

java -Xmx4g -jar /opt/software/snpEff/snpEff.jar download -v GRCm38

java -Xmx4g -jar /opt/software/snpEff/snpEff.jar download -v GRCm38.81

but got the same error

[Pierre Lindenbaum]

mm10 is in snpEff.config

$ curl -sL "https://github.com/pcingola/SnpEff/blob/master/snpEff.config?raw=true" | grep -i mm10
mm10.genome : Mouse

check your snpEff.config file, check the path of this file (i think i'ts option -c (?) in snpEff) , check you're not working behind a proxy.