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Old 04-14-2014, 04:42 AM   #1
qiuyuxinhan
Junior Member
 
Location: China

Join Date: Apr 2014
Posts: 8
Default 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/>
[[email protected] annovar]$ 
How could I solve this problem? Thank you!
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Old 04-17-2014, 06:11 AM   #2
qiuyuxinhan
Junior Member
 
Location: China

Join Date: Apr 2014
Posts: 8
Default

I have solved this problem.
Just type:
[[email protected] annovar]$ chmod a+x annotate_variation.pl

And then type:

[[email protected] 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.
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Old 06-10-2014, 11:03 AM   #3
arcolombo698
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Location: Los Angeles

Join Date: Nov 2013
Posts: 142
Default

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?
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