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!