variant annotation snpeff bosTau7 build

Question

[nuketbilgen]

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

Answer 1

[nuketbilgen]

Hi everyone,

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

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