I have run into a problem that seems simple but has been surprisingly hard. I have a group of .g.vcf.gz files that I want to joint genotype with GATK. They were generated with incorrect and sloppy read set names. I would like to change the name in the header before grouping them together. Unfortunately, I do not have access to a Unix based machine. I have tried to install cygwin for samtools or tabix but my lack of programming has prevented me from getting those programs to work. The other option I explored was decompressing the files, editing the vcf file and then converting back to vcf.gz. The e power of my computer is not great and the large file size has stumpted me.
Can anyone recommend an easy way to change or alter a header?