Big issue with conda to install tabix. conda install tabix will give you r0.2.5 while source code will give you r1.12
(base) [sguo2@login02 htslib-1.12]$ ./tabix
Version: 1.12
Usage: tabix [OPTIONS] [FILE] [REGION [...]]
Indexing Options:
-0, --zero-based coordinates are zero-based
-b, --begin INT column number for region start [4]
-c, --comment CHAR skip comment lines starting with CHAR [null]
-C, --csi generate CSI index for VCF (default is TBI)
-e, --end INT column number for region end (if no end, set INT to -b) [5]
-f, --force overwrite existing index without asking
-m, --min-shift INT set minimal interval size for CSI indices to 2^INT [14]
-p, --preset STR gff, bed, sam, vcf
-s, --sequence INT column number for sequence names (suppressed by -p) [1]
-S, --skip-lines INT skip first INT lines [0]
Querying and other options:
-h, --print-header print also the header lines
-H, --only-header print only the header lines
-l, --list-chroms list chromosome names
-r, --reheader FILE replace the header with the content of FILE
-R, --regions FILE restrict to regions listed in the file
-T, --targets FILE similar to -R but streams rather than index-jumps
-D do not download the index file
--cache INT set cache size to INT megabytes (0 disables) [10]
--separate-regions separate the output by corresponding regions
--verbosity INT set verbosity [3]
(base) [sguo2@login02 htslib-1.12]$ tabix
Program: tabix (TAB-delimited file InderXer)
Version: 0.2.5 (r1005)
Usage: tabix <in.tab.bgz> [region1 [region2 [...]]]
Options: -p STR preset: gff, bed, sam, vcf, psltbl [gff]
-s INT sequence name column [1]
-b INT start column [4]
-e INT end column; can be identical to '-b' [5]
-S INT skip first INT lines [0]
-c CHAR symbol for comment/meta lines [#]
-r FILE replace the header with the content of FILE [null]
-B region1 is a BED file (entire file will be read)
-0 zero-based coordinate
-h print also the header lines
-H print only the header lines
-l list chromosome names
-f force to overwrite the index
Big issue with conda to install tabix. conda install tabix will give you r0.2.5 while source code will give you r1.12