Do anyone know any tool or script to edit the header and add a "chr" prefix to the chromosome name header directly in a .vcf.gz file? I don't want even to uncompress it, since I have the experience that a huge .vcf can't be compressed by bgzip, at least in my computer.
I am working with some genomic files in the .bam and .vcf format, I tried to retrieve some genic regions, and I already sorted that out, beginning with a large one human chromosome .bam file.
When working with that whole chromosome file, I realized that the header had the name of the chromosome without the prefix "chr", only the number, and that gave me a hard time when trying to run mpileup just in the middle of the workflow.
Now, following my working path, I got a big one chromosome .vcf.gz file, which I indexed with tabix in order to retrieve the desired region with ease, but I get the same problem as before, the name of the chromosome is lacking the "chr" prefix, which happens to be not compatible with the .fasta reference file it needs to run the command, just now beginning with a .vcf.gz file.
I thought about going back from .vcf.gz to bam, on which I already know the syntax to edit the headers, but that means doing around four file transformations. That will spend lots of time.
Thanks in advance for any orientation.