Hi all,
I have extracted variation from bam files using samtools, now i want to annotate it using variant effect predictor perl script of EnsEMBL,
[orf@localhost snp_effect_predictor]$ perl variant_effect_predictor.pl -i ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -format vcf -o chr1_.txt -w -b 2000
it did well but applying for next time for another vcf file, i get error
[orf@localhost snp_effect_predictor]$ perl variant_effect_predictor.pl -i ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr2_q20_sort.vcf -format vcf -o chr2_.txt -w -b 2000
-------------------- EXCEPTION --------------------
MSG: Start must be less than or equal to end+1
STACK Bio::EnsEMBL::Feature::new /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/Feature.pm:139
STACK Bio::EnsEMBL::Variation::VariationFeature::new /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm:177
STACK toplevel variant_effect_predictor.pl:304
Ensembl API version = 61
---------------------------------------------------
It says there's may be a problem in vcf file but it worked well for GKUNU9Q04_chr1_q20_sort.vcf. I have used same commands for making vcf file for all chromosomes FYI.
Am i doing anything wrong?
I have extracted variation from bam files using samtools, now i want to annotate it using variant effect predictor perl script of EnsEMBL,
[orf@localhost snp_effect_predictor]$ perl variant_effect_predictor.pl -i ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr1_q20_sort.vcf -format vcf -o chr1_.txt -w -b 2000
it did well but applying for next time for another vcf file, i get error
[orf@localhost snp_effect_predictor]$ perl variant_effect_predictor.pl -i ../samtools-0.1.12a/samfiles/q20/vcf/GKUNU9Q04_chr2_q20_sort.vcf -format vcf -o chr2_.txt -w -b 2000
-------------------- EXCEPTION --------------------
MSG: Start must be less than or equal to end+1
STACK Bio::EnsEMBL::Feature::new /home/orf/EnsEMBL/src/ensembl/modules/Bio/EnsEMBL/Feature.pm:139
STACK Bio::EnsEMBL::Variation::VariationFeature::new /home/orf/EnsEMBL/src/ensembl-variation/modules/Bio/EnsEMBL/Variation/VariationFeature.pm:177
STACK toplevel variant_effect_predictor.pl:304
Ensembl API version = 61
---------------------------------------------------
It says there's may be a problem in vcf file but it worked well for GKUNU9Q04_chr1_q20_sort.vcf. I have used same commands for making vcf file for all chromosomes FYI.
Am i doing anything wrong?