SnpEff build database for Pistachio

0

Entering edit mode

2.1 years ago

Jahad Soorni • 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

build Pistacio database SnpEff • 904 views

ADD COMMENT • link 2.1 years ago by Jahad Soorni • 0

0

Entering edit mode

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 ?

ADD REPLY • link 2.1 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

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.

ADD REPLY • link 2.1 years ago by Jahad Soorni • 0

0

Entering edit mode

sudo : don't do this

ADD REPLY • link 2.1 years ago by Pierre Lindenbaum 161k

0

Entering edit mode

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!

ADD REPLY • link 2.1 years ago by Jahad Soorni • 0

0

Entering edit mode

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

ADD REPLY • link 2.1 years ago by Jahad Soorni • 0

Login before adding your answer.