Question: SnpEff output searching for specific genes
2
gravatar for federico.bernuzzi
14 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 wrote:

Hi,

I have successfully runned SnpEff. The ouput VCF file contains 2.5 million "lines", data sets. I wanted to ask if someone is interested in looking at only a couple of genes how would I go about doing this? In addition is there a chance than the output VCF file can be transported into a different programme for example excel?

Many thanks

FB

rna-seq snp galaxy • 587 views
ADD COMMENTlink modified 14 months ago by Guy Reeves1.0k • written 14 months ago by federico.bernuzzi20
1
gravatar for Guy Reeves
14 months ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

maybe you can use 'VCF-BEDintersect:' tool to slice out the genes using their coordinates in a BED file or you can type the interval in. Cheers Guy

ADD COMMENTlink written 14 months ago by Guy Reeves1.0k

Agree - another good choice!

ADD REPLYlink written 14 months ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
14 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool Select can be used to pull out lines that match a specific text string such as a gene ID. There are other data manipulation tools that can filter data by matching text or chromosome coordinates (example: VCFfilter).

VCF is a special version of tabular data, so importing into Excel or other spreadsheet applications is definitely possible. Download the data and change the file extension to be ".txt" or ".tabular". Remove the header before or after downloading or set those lines as a header within the downstream application. The same Select tool can be used to remove header lines in Galaxy ("not matching" the pattern ^#).

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 14 months ago by Jennifer Hillman Jackson25k
0
gravatar for federico.bernuzzi
14 months ago by
Quadram Institute of BioSciences
federico.bernuzzi20 wrote:

Many thanks for the reply I shall look into it.

ADD COMMENTlink written 14 months ago by federico.bernuzzi20
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