Hello,
I'm using annovar for the first time. I started by running the example provided in the ANNOVAR website. I got no problem, so I probably don't have a problem with the software, the version...
Now I'm trying it on my data. I started with a very short tab-delimitated file:
or
I think that the "comments" column is not mandatory ; am I right ?
In the example, the file was:
I don't see any difference between the two files, so the problem should not come from my file.
I also pay attention to be in the correct folder :
Here are the command lines that I used in both cases:
The error message shown below seems to indicate that I provided the wrong input.
Does someone see where is my problem ?
Thanks for any help !
I'm using annovar for the first time. I started by running the example provided in the ANNOVAR website. I got no problem, so I probably don't have a problem with the software, the version...
Now I'm trying it on my data. I started with a very short tab-delimitated file:
1 6589054 6589231 A S
1 6589054 6589231 A S comments: rs1000050, a SNP in Illumina SNP arrays
In the example, the file was:
1 161003087 161003087 C T comments: rs1000050, a SNP in Illumina SNP arrays
I also pay attention to be in the correct folder :
[... annovar]# ls
annotate_variation.pl coding_change.pl example retrieve_seq_from_fasta.pl VICJE_nonsense211011
auto_annovar.pl convert2annovar.pl humandb summarize_annovar.pl
[... annovar]# cd VICJE_nonsense211011/
[... VICJE_nonsense211011]# ls
VICJE_nonsense VICJE_nonsense~ VICJE_nonsense.txt~
annotate_variation.pl coding_change.pl example retrieve_seq_from_fasta.pl VICJE_nonsense211011
auto_annovar.pl convert2annovar.pl humandb summarize_annovar.pl
[... annovar]# cd VICJE_nonsense211011/
[... VICJE_nonsense211011]# ls
VICJE_nonsense VICJE_nonsense~ VICJE_nonsense.txt~
perl annotate_variation.pl -geneanno example/ex1.human humandb/
perl annotate_variation.pl -geneanno VICJE_nonsense211011/VICJE_nonsense
perl annotate_variation.pl -geneanno VICJE_nonsense211011/VICJE_nonsense
Does someone see where is my problem ?
Thanks for any help !
Code:
[... annovar]# perl annotate_variation.pl -geneanno VICJE_nonsense211011/VICJE_nonsense Syntax error Usage: annotate_variation.pl [arguments] <query-file|table-name> <database-location> Optional arguments: -h, --help print help message -m, --man print complete documentation -v, --verbose use verbose output Arguments to download databases or perform annotations --downdb download UCSC Genome Browser annotation database --geneanno annotate variants by functional consequences on genes --regionanno annotate variants by targetting specific genomics regions --filter filter variants based on a position list --webfrom <string> specify the source of database (default usually works fine) Arguments to control input and output --outfile <file> output file prefix --zerostart input query file uses half-open zero-start coordinate --dbtype <string> database type --buildver <string> genome build version (default: hg18 for human) --gff3dbfile <file> specify the GFF3 DB file used in region-based annotation --genericdbfile <file> specify the generic DB file used in filter-based annotation --vcfdbfile <file> specify the DB file in VCF format in filter-based annotation --bedfile <file> specify a BED file in region-based annotation --time print out local time during program run --separate separately print out all function of a variant (default: one line per variant) --colsWanted <string> specify which columns to output in -regionanno by comma-delimited numbers --comment print out comment line (those starting with #) in output files --scorecolumn <int> the column with scores in database file (for region-based annotation) --exonsort sort the exon number in output line (for gene-based annotation) --transcript_function use transcript name rather than gene name in gene-based annotation output --hgvs use HGVS format for exonic annotation (c.122C>T rather than c.C122T) Arguments to fine-tune the annotation procedure --batchsize <int> batch size for processing variants per batch (default: 5m) --genomebinsize <int> bin size to speed up search (default: 100k for -geneanno, 10k for -regionanno) --expandbin <int> check nearby bin to find neighboring genes (default: 2m/genomebinsize) --neargene <int> distance threshold to define upstream/downstream of a gene --score_threshold <float> minimum score of DB regions to use in annotation --reverse reverse directionality to compare to score_threshold --normscore_threshold <float> minimum normalized score of DB regions to use in annotation --rawscore output includes the raw score (not normalized score) in UCSC Browser Track --minqueryfrac <float> minimum percentage of query overlap to define match to DB (default: 0) --splicing_threshold <int> distance between splicing variants and exon/intron boundary (default: 2) --maf_threshold <float> filter 1000G variants with MAF above this threshold (default: 0) --sift_threshold <float> SIFT threshold for deleterious prediction (default: 0.05) --precedence <string> comma-delimited to specify precedence of variant function (default: exonic>intronic...) Arguments to control memory usage --memfree <int> ensure minimum amount of free system memory (default: 100000, in the order of kb) --memtotal <int> limit total amount of memory used by ANNOVAR (default: 0, unlimited, in the order of kb) --chromosome <string> examine these specific chromosomes in database file Function: annotate a list of genetic variants against genome annotation databases saved at local disk. Example: #download gene annotation database (for hg18 build) and save to humandb/ directory annotate_variation.pl -downdb gene humandb/ annotate_variation.pl -buildver mm9 -downdb mce30way mousedb/ annotate_variation.pl -downdb snp130 humandb/ #gene-based annotation of variants in the varlist file (by default --geneanno is ON) annotate_variation.pl ex1.human humandb/ #region-based annotate variants annotate_variation.pl -regionanno -dbtype mce44way ex1.human humandb/ annotate_variation.pl -regionanno -dbtype gff3 -gff3dbfile tfbs.gff3 ex1.human humandb/ #filter rare or unreported variants (in 1000G/dbSNP) or predicted deleterious variants annotate_variation.pl -filter -dbtype 1000g_ceu -maf 0.01 ex1.human humandb/ annotate_variation.pl -filter -dbtype snp130 ex1.human humandb/ annotate_variation.pl -filter -dbtype avsift ex1.human humandb/ Version: $LastChangedDate: 2011-10-02 22:13:18 -0700 (Sun, 02 Oct 2011) $
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