vcf to xls wrong columns

Question

[cristina_sabiers]

This is probaly a silly question and easy to fix...for most of all of you XD

When I open my vcf file on excel sometimes get mismatches like above (line 10) is any easy way to fix it and not manually?

ID  REF   ALT  QUAL   FILTER    INFO            
0   T   <CNV>   100     PASS    PRECISE=FALSE   
0   A   <CNV>   100     PASS    PRECISE=FALSE   
0   G   T      342.83   PASS    AF=0.493902         
0   A   G      1810.86  PASS    AF=1            
0   C   G      147.37   PASS    AF=1                    
0   A   G      1096.97  PASS    AF=1           
0   A   G      604.62   PASS    AF=1                  
0   C   G     189.44    PASS    AF=0.956522 
0   A   C     1561.91   PASS    AF=1    
0   C   CG    CGG       51.23   PASS    
0   A   G     726.95    PASS    AF=1    
0   T   C     770.16    PASS    AF=0.927835 
0   T   C     928.45    PASS    AF=1

Thanks!

[Pierre Lindenbaum]

genomax2+1: you used tab AND the comma as delimiter when importing. a multi ALT allele was split [CG,CGG]

and please, please, don't use excel.

Want to know something terrifying? There are people currently analysing whole exome variant data using Excel. I kid you not.

— Daniel MacArthur (@dgmacarthur) October 25, 2012

[cristina_sabiers]

what I can use instead excel?

[dovah]

A text editor would be more apporpriate. What OS are you working on?

[cristina_sabiers]

Thanks dovah for your answer, couldnt write before because I have been pretty bussy, I use ubuntu. Im quiet new on all of this, just try to learn on my own thats because mostly I ask for silly questions...

Thanks to my boss I got few bam, fastq files and reports from another company, the reports are all in excel, thats the main reason why I ask to have in that format, if is another better I will use whatever more usefull.

Thanks!!!

[WouterDeCoster]

http://genomecomb.sourceforge.net/ has a tool to display tabular data (cg viz - http://genomecomb.sourceforge.net/docs/cg_viz.html) . Developed in-house here, doesn't work with vcf files but with tab separated file with chromosome begin and end of features and all sort of annotations. Slightly different format than vcf... Ideal for querying and all sort of manipulations.

It's pretty damn amazing but alas not written in a frequently used language (Tcl)

[cristina_sabiers]

Thanks Wouter I will look later at home the links you provided to me :)

Im pretty new in all of this, so I just have tutorials from internet and people like you who help me.

I really apreciate the help of all of you!!!

[Pierre Lindenbaum]

linux command line, R, galaxy. If your really need a graphical interface, using something like http://www.knime.org

[GenoMax]

Are you "importing" the file (so you can choose an appropriate delimiter, e.g. tab) in instead of just opening it in Excel? That should work better.

[cristina_sabiers]

I just open the vcf on excel, rename the file....seems then I do wrong

[GenoMax]

You can use excel, if you want. It is fine to use it to look at files.

Use "file import" instead of just opening the file directly and then make sure only "tab" delimited is checked as @Pierre mentioned above.

[WouterDeCoster]

Indeed fine to look at files, but I wouldn't encourage to use excel for manipulation or analysis. May yield unexpected results and very bad for reproducibility (tracking what you have done).

[dovah]

@ cristina_sabiers : is there a specific reason why you have to do it in excel?

[cristina_sabiers]

no...

I thought was the way to do so, I got the reports like I told in my other message on excel files,

They even put predictors on the excel file, so I can use filters on the gens to look only at damage gens or what I want... :)

[cristina_sabiers]

thanks I will try later at eveening importing instead.