where can I found ecab3.0 SNP annotation?

Question

[mary]

Hi every one, I appreciate if someone helps me. I am trying to make PFB file for CNV analysis in horse. So where can I find SNP annotation file of Equ Cab 3 . any suggestion will be appreciate.

[GenoMax]

Ensembl has the VCF files for horse here.

[mary]

Thanks a lot for your reply. there is three file for equus caballus here, when I extract them they have more than 65167 SNP. so I am confusing now, I have a litter familiar with VCF format so, which file in a file that I can remap with that my old map file?

Answer 1

[mmunsanbioinfo]

#Descargar base de datos EquCab3 
java -jar $HOME/snpEff/snpEff.jar download EquCab3.0.99


#Anotacion de los vcf y con salida de estadisticas csv
java -Xmx20g -jar $HOME/snpEff/snpEff.jar -csvStats INDELs_stats.csv -c $HOME/snpEff/snpEff.config -v -o gatk EquCab3.0.99  PRE_PASS_INDEL.vcf > PRE_PASS_INDEL_ANN.vcf

# No gatk format
java -Xmx20g -jar $HOME/snpEff/snpEff.jar -csvStats INDELs_stats.csv -c $HOME/snpEff/snpEff.config -v  EquCab3.0.99  PRE_PASS_INDEL.vcf > PRE_PASS_INDEL_ANN.vcf