Well, I'm rather sure that the problem came from the strand. I rerun ANNOVAR without the reverse sense information and I got no more this warning:
The point is that I don't want to loose half of the information...
Could you suggest me something?
perl ./annotate_variation.pl -geneanno $dir/$file humandb -build hg19
NOTICE: Reading gene annotation from humandb/hg19_refGene.txt ... Done with 38781 transcripts (including 6123 without coding sequence annotation) for 23261 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_refGeneMrna.fa ... Done with 160 sequences
WARNING: A total of 319 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Finished gene-based annotation on 94 genetic variants in VICJE_missense211011/VICJE_strand_file
NOTICE: Output files were written to VICJE_missense211011/VICJE_strand_file.variant_function, VICJE_missense211011/VICJE_strand_file.exonic_variant_function
NOTICE: Reading gene annotation from humandb/hg19_refGene.txt ... Done with 38781 transcripts (including 6123 without coding sequence annotation) for 23261 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_refGeneMrna.fa ... Done with 160 sequences
WARNING: A total of 319 sequences will be ignored due to lack of correct ORF annotation
NOTICE: Finished gene-based annotation on 94 genetic variants in VICJE_missense211011/VICJE_strand_file
NOTICE: Output files were written to VICJE_missense211011/VICJE_strand_file.variant_function, VICJE_missense211011/VICJE_strand_file.exonic_variant_function
Could you suggest me something?
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