Hello. Thank you in advance, I successfully ran ANNOVAR, but have a question regarding the NOTICE from the output, and wish to understand.
perl table_annovar.pl example/Sample_UYYY-122_flt.avinput humandb/ -buildver hg19 -out MYANNO -remove -protocol refGene,phastConsElements46way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,ljb2_all -operation g,r,r,f,f,f,f -nastring NA -csvout
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NOTICE: Processing operation=g protocol=refGene
NOTICE: Reading gene annotation from humandb/hg19_refGene.txt ... Done with 46966 transcripts (including 9362 without coding sequence annotation) for 24933 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_refGeneMrna.fa ... Done with 14282 sequences
WARNING: A total of 301 sequences will be ignored due to lack of correct ORF annotation
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WARNING: 3 exonic SNPs have WRONG reference alleles specified in your input file!
WARNING: An example input line is <chr1 206566048 206566048 G het 47 30>
WARNING: ANNOVAR can still annotate exonic_variant_function for the mutation correctly!
WARNING: you may have used wrong -buildver, or specified incorrect reference allele, or used outdated mRNA FASTA file!
I just wish to understand where these WARNINGS are coming from and how to fix them.
1) I checked my mRNA.fa file and it is up to date
2) This must mean there are just code errors in my VCF file?
perl table_annovar.pl example/Sample_UYYY-122_flt.avinput humandb/ -buildver hg19 -out MYANNO -remove -protocol refGene,phastConsElements46way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,ljb2_all -operation g,r,r,f,f,f,f -nastring NA -csvout
-----------------------------------------------------------------
NOTICE: Processing operation=g protocol=refGene
NOTICE: Reading gene annotation from humandb/hg19_refGene.txt ... Done with 46966 transcripts (including 9362 without coding sequence annotation) for 24933 unique genes
NOTICE: Reading FASTA sequences from humandb/hg19_refGeneMrna.fa ... Done with 14282 sequences
WARNING: A total of 301 sequences will be ignored due to lack of correct ORF annotation
---------------------------------------------------------------------------------------
WARNING: 3 exonic SNPs have WRONG reference alleles specified in your input file!
WARNING: An example input line is <chr1 206566048 206566048 G het 47 30>
WARNING: ANNOVAR can still annotate exonic_variant_function for the mutation correctly!
WARNING: you may have used wrong -buildver, or specified incorrect reference allele, or used outdated mRNA FASTA file!
I just wish to understand where these WARNINGS are coming from and how to fix them.
1) I checked my mRNA.fa file and it is up to date
2) This must mean there are just code errors in my VCF file?