Entering edit mode
2.0 years ago
Jahad Soorni
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0
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
why? what's your input ? what are the available/missing data that could be used to build a snpEff database ?
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.sudo
: don't do thisI 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!
Thanks Pierre. I add some information below. The pistachio genome is at scafold level.