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Question: gene names from a vcf annotate file
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gravatar for 1603.neha
2.5 years ago by
1603.neha • 70
1603.neha • 70 wrote:

hi i need an answer.

i have a vcf file and i want to see gene names on each chromosomes in the vcf file in a tabluar format

I need it urgent asap please

thanks in advance for helping

bwa snp galaxy • 1.9k views
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modified 2.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.5 years ago by 1603.neha • 70
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gravatar for christophe.habib
2.5 years ago by
christophe.habib • 340
France
christophe.habib • 340 wrote:

What you need is to annotate your vcf file. Depending on where you are working you can search for tool available to do so. Annovar can do the job.
ADD COMMENT • link written 2.5 years ago by christophe.habib • 340
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gravatar for Jennifer Hillman Jackson
2.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

If after adding in Gene name annotation, see the tools in the group NGS: VCF Manipulation to filter content. For example, try VCFfilter or VCFtoTab-delimited followed by Cut, Filter/Select, Group.

Thanks, Jen, Galaxy team
ADD COMMENT • link written 2.5 years ago by Jennifer Hillman Jackson ♦ 25k

I think there is an option in annovar to specify the output format as tabular. Unfortunately the tabular file lacks some column (such as GT:AD:DP:GQ:PL column and the following one).

If you ask the output as vcf, Annovar put all annotations in 1 column (INFO) to respect the VCF format file, it is not easy to read. The VCFtoTab-delimited seems to make the work. But if you compare the VCF produced by annovar and the tabular file obtained with this tools you can see that it lacks some informations (in the AAChange.refGene column for example).

Since I wasn't sure about the reason of these differences, I made a script to parse the VCF file in my own way. Jen, do you know if these blank field (that shouldn't be blank) is a normal behaviour ?

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by christophe.habib • 340

Sorry, I missed this comment before.

Annovar only parses out certain data. The other tools I mention will parse out the full content. Also, Annovar is set up at http://usegalaxy.org with indexes for certain genomes. The NGS: VCF Manipulation tools will work with any genome/transcriptome/exome (including custom loaded e.g. "Custom genomes") as they are not dependent on pre-computed indexes.

ADD REPLY • link written 18 months ago by Jennifer Hillman Jackson ♦ 25k
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