In the course of getting VCF tools running on Mac (OSX), I stumbled upon what appears to be a Mac-specific problem with tabix. The VCFtools merge-vcf perl script calls tabix <filename.vcf> -l . The '-l' option is not listed in the tabix manual document, but it is supposed to list the sequence names stored in the index of the bgzipped vcf file that gets created via 'tabix -p vcf <filename.vcf.gz>' . Whether running merge-vcf or running tabix directly on the bgzipped versions of the VCFtools example files (as well as on my own data), on a Mac I get the following error:
'[main] invalid region: unknown target name or minus interval.'
But, when I run the same exact commands on a Linux machine....everything works fine, no errors at all.
No related posts to date as far as I can tell, but is anyone else aware of this issue, and is there any plan to correct it in the future?
'[main] invalid region: unknown target name or minus interval.'
But, when I run the same exact commands on a Linux machine....everything works fine, no errors at all.
No related posts to date as far as I can tell, but is anyone else aware of this issue, and is there any plan to correct it in the future?
Comment