Question: Failed Annotating The Example Vcf File In The Installation Folder Of Vcftools
0
gravatar for Jianfengmao
9.7 years ago by
Jianfengmao310
Jianfengmao310 wrote:

Dear BioStarers,

I need your helps on fixing problems I faced when annotating the example vcf file (annotate.txt) in the installation folder of VCFtools. I have listed the commands I used and the results I got.

Also, I want to know what type of annotation information file it (VCFtools) supported, gff file or others?

cat annotate-test.vcf | vcf-annotate -a annotate.txt -d
key=INFO,ID=ANN,Number=1,Type=Integer,Description='My custom
annotation' | bgzip -c > annout.vcf.gz
Can't use an undefined value as an ARRAY reference at
/ebio/abt6_projects/backup/solexa_tools/VCFtools/bin/vcf-annotate line
134.
vcf annotation • 3.4k views
ADD COMMENTlink modified 9.7 years ago by Raony Guimaraes100 • written 9.7 years ago by Jianfengmao310
1

what is your 'VCFtools' ? I cannot see a 'vcf-annotate' in http://vcftools.sourceforge.net/options.html

ADD REPLYlink written 9.7 years ago by Pierre Lindenbaum130k

Which version of VCFtools did you use, remeber to always mention the version!

ADD REPLYlink written 9.7 years ago by Michael Dondrup47k
0
gravatar for Hamish
8.6 years ago by
Hamish3.1k
UK
Hamish3.1k wrote:

The vcf-annotate script is described in the "VCFtools: Perl tools and API" documentation. The annotations file is a tab-delimited file, which has been compressed and indexed with tabix (part of samtools). I suspect your error message relates to attempting to use a, presumably un-indexed, text file as input for the annotations.

The annotation format is described in the documentation, and additional information can be found in the script's help message, available using:

vcf-annotate -h
ADD COMMENTlink modified 12 months ago by RamRS30k • written 8.6 years ago by Hamish3.1k
0
gravatar for Raony Guimaraes
8.6 years ago by
Raony Guimaraes100 wrote:

Hello, I end up using a lot more VariantAnnotator from GATK to treat my VCF files against anything I really want. I gave up using vcf-annotate, it's not very functional...

Right now I'm annotating using 1000genomes(nov2011), dbsnp135, Exome Variation Server, snpeff. And after this I also created a python script to include some annotations made with annovar (SIFT and Polyphen for example)

My big command:

command = "java -Xmx4G -jar ~/lgc/programs/GenomeAnalysisTK-1.4-30-gf2ef8d1/Geno
meAnalysisTK.jar 
-T VariantAnnotator 
-R ~/lgc/datasets/gatk_data/b37/human_g1k_v37.fasta 
-A SnpEff 
--variant %s 
--snpEffFile snpEff_output.vcf 
-L %s 
-o %s.snpeff.dbsnp135.exomeserver.vcf 
--dbsnp /home/raony/lgc/datasets/dbsnp/dbsnp-135.vcf 
--resource:dbsnp135 /lgc/datasets/dbsnp/dbsnp-135.vcf 
--resource:exome_server /lgc/datasets/exome_variation_server/ESP5400.snps.vcf 
--resource:1000genomes /lgc/datasets/1000new_release/ALL.wgs.phase1_release_v2.20101123.snps_indels_sv.sites.vcf 
-E 1000genomes.AF 
-E dbsnp135.GMAF 
-E dbsnp135.dbSNPBuildID 
-E exome_server.AAC 
-E exome_server.GS 
-E exome_server.PP 
-E exome_server.CDP 
-E exome_server.MAF" % (options.vcf_file, options.vcf_file, filename)

It's very useful specially when we are receiving VCF Files from different centers and I want to include the same annotations that we use in house.

ADD COMMENTlink modified 12 months ago by RamRS30k • written 8.6 years ago by Raony Guimaraes100
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