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  • annovar error with table_annovar.pl line 214

    Hi, guys. I'm a newer for using the annovar. Now I meet a problem which makes me going crazy. Please do me a favor. Thank you very much!

    PHP Code:
    [nep@mu01 annovar]$ ls
    annotate_variation
    .pl  D2364.vcf                   summarize_annovar.pl
    annovar_downdb
    .log     example                     table_annovar.pl
    coding_change
    .pl       humandb                     variants_reduction.pl
    convert2annovar
    .pl     retrieve_seq_from_fasta.pl  wget-log
    [nep@mu01 annovar]$ perl convert2annovar.pl -format vcf4 D2364.vcf D2364.avin
    put
    NOTICE
    Finished reading 27930 lines from VCF file
    NOTICE
    A total of 27697 locus in VCF file passed QC thresholdrepresenting 26954 SNPs (18940 transitions and 8014 transversions) and 1013 indels/substitutions
    NOTICE
    Finished writting 26924 SNPs (18931 transitions and 7993 transversions) and 1011 indels/substitutions for 1 sample
    [nep@mu01 annovar]$ perl table_annovar.pl D2364.avinput humandb/ -buildver hg19 -protocol refGene,knownGene,ensGene,gerp++elem,phastConsElements46way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,snp137,snp137NonFlagged,avsift,ljb2_all,clinvar_20140211  -operation g,g,g,r,r,r,f,f,f,f,f,f,f,-csvout
    -----------------------------------------------------------------
    NOTICEProcessing operation=g protocol=refGene
    Can
    't exec "annotate_variation.pl": Permission denied at table_annovar.pl line 214.
    Error running system command: <annotate_variation.pl -geneanno -buildver hg19 -dbtype refGene -outfile D2364.avinput.refGene -exonsort D2364.avinput humandb/>
    [nep@mu01 annovar]$ 
    How could I solve this problem? Thank you!

  • #2
    I have solved this problem.
    Just type:
    [nep@mu01 annovar]$ chmod a+x annotate_variation.pl

    And then type:

    [nep@mu01 annovar]$perl table_annovar.pl D2364.avinput humandb/ -buildver hg19 -protocol refGene,knownGene,ensGene,gerp++elem,phastConsElements46way,genomicSuperDups,esp6500si_all,1000g2012apr_all,snp135,snp137,snp137NonFlagged,avsift,ljb2_all,clinvar_20140211 -operation g,g,g,r,r,r,f,f,f,f,f,f,f,f -csvout

    This time will be OK.

    Comment


    • #3
      I have a question regarding annovar, i can create a new thread, as well..

      Do you know how to display the depth score from the vcf file into the table_annovar

      On my end I see the depth information on the .avinput file, but it is not scored onto the table_Annovar.pl as a column

      how do I get the dp information from the input file onto the multianno.txt file?

      Comment

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