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Question: VCF gene name sorting
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gravatar for nbhassou
3.1 years ago by
nbhassou • 10
United States
nbhassou • 10 wrote:

Hello,

I have a vcf file and need to tie it to the gene name. I did this with the vcf annotate tool using the hg19 genome as the BED file. The gene name is in the info field of the vcf file. But now I need to find the gene with the most polymorphisms. I don't know how to do this without delimiting first, but when I try doing this the convert tool ends up just lining up the text in each cell back to back, and it is no longer in a table-like format. How can I get around this?

 

Thanks,

Nadia
gene name vcf • 1.3k views
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modified 3.1 years ago • written 3.1 years ago by nbhassou • 10
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gravatar for Jennifer Hillman Jackson
3.1 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Are you converting the VCF to tabular format with the tool VCFtoTab-delimited on http://usegalaxy.org? I just retested all options and it seems to be parsing out VFC fields distinctly without problems. 

Maybe post a snippet of a few of the lines and we can see if there is an obvious format problem? Or you can share a history and send that link to galaxy-bugs@lists.galaxyproject.org. Include a link to this post and note which datasets are the problem (just so we are looking at the same thing).

Thanks! Jen, Galaxy team
ADD COMMENT • link written 3.1 years ago by Jennifer Hillman Jackson ♦ 25k
0
gravatar for nbhassou
3.1 years ago by
nbhassou • 10
United States
nbhassou • 10 wrote:

Hello,

 

This is an example of what I am getting: 

fileformat=VCFv4.1 ##fileDate=20151018 ##source=freeBayes v0.9.20 ##reference=/galaxy/data/hg19/sam_index/hg19.fa ##phasing=none ##commandline="freebayes --bam localbam_0.bam --fasta-reference /galaxy/data/hg19/sam_index/hg19.fa --vcf /galaxy-repl/main/fil

This occurred after trying to join two tabular files, but I see the same thing when trying to tab delimit on the annotated vcf. It is bold, larger font and with no order. 
ADD COMMENT • link written 3.1 years ago by nbhassou • 10
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