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?
#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?