where can I found ecab3.0 SNP annotation?
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16 months ago
mary ▴ 210

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.

snp genome ecab3.0 • 328 views
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Ensembl has the VCF files for horse here.

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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?

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5 weeks ago
#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
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