variant annotation snpeff bosTau7 build
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Entering edit mode
6.0 years ago
nuketbilgen ▴ 40

Hi everyone!

The highly unlikely situation happened.

My next generation seq. data have been aligned to bosTau7 build. 

I am having troubles on building data set for that. And when I use lift up the vcf file with USCS bosTau7 build  to UMD3.1 snpeff does not give me any annotation (the error different reference genome)

I downloaded gff file from the link below also tried ucsc to get gff file.

http://128.206.12.216/drupal/sites/bovinegenome.org/files/data/btau_4.6.1/Ensembl75_liftOver_Btau_4.6.1_genes.gff3.gz

I have the bosTau7.fa

I am getting the error "java.lang.RuntimeException: Property: 'bosTau7.genome' not found"

vi snpEffect.config

# Bos_taurus genome: bosTaurus7
 bosTau7.genome : Bos_taurus

esc
 :w
 :x

java -jar snpEff.jar build -gff3 bosTau7 or java -jar snpEff.jar build bosTau7

Thank you

snpeff variant annotation bosTaurus7 • 1.8k views
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0
Entering edit mode
6.0 years ago
nuketbilgen ▴ 40

Hi everyone,

I solved it! just needed to ad -c snpEffect.config

java -jar snpEff.jar build -c snpEffect.config -refSeq -v bosTau7

 

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