I’m interested in using GeneticVariation.jl to work with VCF files. My VCF files are compressed with bgzip and are indexed using tabix.
I’m looking at the documentation for reading in VCF files here: https://github.com/BioJulia/GeneticVariation.jl/blob/master/docs/src/io/vcf-bcf.md . The document suggests to me that the VCF reader should be used with uncompressed VCF’s.
It is my understanding that I could change
reader = VCF.Reader(open("example.vcf", "r"))
reader = VCF.Reader(open(`zless example.vcf.gz`, "r"))
To read in a compressed VCF. Is this the recommended way for working with compressed VCF files? It seems that there’s a reader for BCF files as well, though I’d rather not have to convert all of my vcf.gz files to bcfs.