Adding header to VCF and combine VCF
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5.4 years ago
basalganglia ▴ 40

Hello everyone,

 

I want to ask that I need add following column to my VCF. For this, I get vcf file to my desktop with Filezilla and open with excel and add following. Does ıt modıfy VCF file? How can I do with another way?

##fileformat=VCFv4.1

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample_name

 

Another question is about chromosome order. I want to combine VCF files with GATK and CombineVAriants command. It needs cotig file order from 1 ,2 3,.....,22,X,Y. But my contig file in VCF as X,1,2,3,....,22. How can I solve this problem ?

 

Does it work if I get VCF file to my desktop with FTP and open with Excel and carry all X variants to end of the Excel file. Is there another way to solve this problem?

 

Thanks,

 

BG

 

myposts vcf combine vcf vcf opening with excel • 3.2k views
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What Pierre is trying to say, more explicitly, is that working with genomics data more-or-less requires some scripting in R, python, perl, or bash (or a combination thereof) and use of third-party tools that really run best on the command-line. Therefore, you can 1) find a bioinformatics collaborator to help you with your problem or 2) learn to do this yourself or 3) a combination of 1 and 2.

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