I did variant calling using BWA + PiCard + GATK and have just got the filtered VCF files from GATK. In the process of running GATK, I used list of inputs (11 samples) and for most steps, I had only one output file for each step. Now, I got two VCF files (one for SNPs and the other is for indels), each of which contains 11 samples. I can see the names of the 11 samples in the header of vcf files, and each sample seems to have one column of data. So I am wondering how to split each VCF files into individual sample vcf files?
From my search, vcf tools seems to have the capability of splitting vcf, but I could not find an example for splitting multiple samples. Can someone please help me? Thanks a lot