I am trying to use vcf-merge. In a separate directory with all files of interest, I have compressed them with bgzip (from a shell script), so they all now have the .gz extension. One must then index these compressed files with the tabix command. On vcf tools, it specifically states that "tabix -p" should be used. To test this out, I used this on two VCF compressed files in another directory, but I got an error message, which reads, "[main] unrecognized preset 'filename.vcf.gz'." However, if I just use "tabix" on the compressed test files, I see the corresponding .tbi file for each .gz file.

Is it all right to just use "tabix" on the compressed files in a shell script, or am I missing a step to use vcf-merge? It states in documentation that VCF files must be position sorted, but I though that these files are already sorted or in position order before compressing.

Thank you for any help.