This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html
I managed to get both a .csi and a .tbi file that were totally identical except for filename! I think perhaps bcftools is just bugged here, and it is infact already writing tbi (assuiming vcf.gz of course, as tbi wouldn't work on bcf).
I was unable to reproduce this when doing my PR to resolve that issue, but I just reproduced it again by accident and it's more nuanced than I reported before.
bcftools index -m 0 foo.vcf.gz writes a tabix index to foo.vcf.gz.csi. Running tabix foo.vcf.gz writes a byte identical index to foo.vcf.gz.tbi. This is a minor buglet where the index command ought to name the output accordingly. It's very minor, but something to add to the list.
pd3
commented
2 months ago
My own comment from #2008
I was unable to reproduce this when doing my PR to resolve that issue, but I just reproduced it again by accident and it's more nuanced than I reported before.
bcftools index -m 0 foo.vcf.gzwrites a tabix index to foo.vcf.gz.csi. Runningtabix foo.vcf.gzwrites a byte identical index to foo.vcf.gz.tbi. This is a minor buglet where the index command ought to name the output accordingly. It's very minor, but something to add to the list.