Hi all,
I was wondering which is the easiest way to merge multiple vcf files (outputs of Varscan). I have some vcf files listing all the called snps for an individual (1 snp per line). I would like to put together all this info in a n output that shows for every line a snp (original base, variant base/bases, and eventually number of individuals sharing the variant).
I tried with GATK CombineVariants and had the ouput I wanted, but in case of different variant at the same position, only one of the variant bases was reported.
I am working on a Mac's Terminal, OS 10.6.
If needed I have access also to a Linux OS.
Thanks in advance!
I was wondering which is the easiest way to merge multiple vcf files (outputs of Varscan). I have some vcf files listing all the called snps for an individual (1 snp per line). I would like to put together all this info in a n output that shows for every line a snp (original base, variant base/bases, and eventually number of individuals sharing the variant).
I tried with GATK CombineVariants and had the ouput I wanted, but in case of different variant at the same position, only one of the variant bases was reported.
I am working on a Mac's Terminal, OS 10.6.
If needed I have access also to a Linux OS.
Thanks in advance!
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