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SnpEff build database for Pistachio

Hi, We are going to building a database for Pistachio to annotaion of our filtered.vcf files. However we couldn't create it using SnpEff. Can anyone a suggestion? Thanks

build pistacio database snpeff
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written by Jahad Soorni • Jahad Soorni

However we couldn't create it using SnpEff.

why? what's your input ? what are the available/missing data that could be used to build a snpEff database ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre, When I run this command sudo java -jar snpEff.jar build -gff3 -v PisVer_v2, first I get this error "WARNING_TRANSCRIPT_NOT_FOUND: Too many 'WARNING_TRANSCRIPT_NOT_FOUND' warnings, no further warnings will be shown.", then " Too many 'WARNING_GENE_COORDINATES' warnings, no further warnings will be shown." and finally it prompt that the database not build. The input file is gff file at this link GCF_008641045.1_PisVer_v2_genomic.gff.gz and genome ref at GCF_008641045.1_PisVer_v2_genomic.fna.gz.

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written by Jahad Soorni • Jahad Soorni

I didn't use sudo, but we get the same error. I guss our folders and file names and locations are incorrect, but I don't which of them!

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written by Jahad Soorni • Jahad Soorni

Thanks Pierre. I add some information below. The pistachio genome is at scafold level.

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written by Jahad Soorni • Jahad Soorni

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