annovar error with table_annovar.pl line 214

[qiuyuxinhan]

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!

[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 threshold, representing 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,f -csvout
-----------------------------------------------------------------
NOTICE: Processing 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!

[qiuyuxinhan]

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.

[arcolombo698]

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?