Question: vcf to xls wrong columns
0
gravatar for cristina_sabiers
2.3 years ago by
Spain
cristina_sabiers40 wrote:

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!

vcf • 706 views
ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by cristina_sabiers40
4

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.

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum114k

what I can use instead excel?

ADD REPLYlink written 2.3 years ago by cristina_sabiers40
1

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

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by dovah30

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!!!

ADD REPLYlink written 2.3 years ago by cristina_sabiers40
1

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)

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by WouterDeCoster33k

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!!!

ADD REPLYlink written 2.3 years ago by cristina_sabiers40

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

ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum114k
1

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.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by genomax58k

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

ADD REPLYlink written 2.3 years ago by cristina_sabiers40
2

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.

ADD REPLYlink written 2.3 years ago by genomax58k

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).

ADD REPLYlink written 2.3 years ago by WouterDeCoster33k

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

ADD REPLYlink written 2.3 years ago by dovah30

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... :)

ADD REPLYlink written 2.3 years ago by cristina_sabiers40

thanks I will try later at eveening importing instead.

ADD REPLYlink written 2.3 years ago by cristina_sabiers40
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