bgzip – Block compression/decompression utility
tabix – Generic indexer for TAB-delimited genome position files
bgzip [-cdhB] [-b virtualOffset] [-s size] [file]
tabix [-0lf] [-p gff|bed|sam|vcf] [-s seqCol] [-b begCol] [-e endCol] [-S lineSkip] [-c metaChar] in.tab.bgz [region1 [region2 [...]]]
Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line. The input data file must be position sorted and compressed by bgzip which has a gzip(1) like interface. After indexing, tabix is able to quickly retrieve data lines overlapping regions specified in the format "chr:beginPos-endPos". Fast data retrieval also works over network if URI is given as a file name and in this case the index file will be downloaded if it is not present locally.
Input format for indexing. Valid values are: gff, bed, sam, vcf and psltab. This option should not be applied together with any of -s, -b, -e, -c and -0; it is not used for data retrieval because this setting is stored in the index file. [gff]
Column of sequence name. Option -s, -b, -e, -S, -c and -0 are all stored in the index file and thus not used in data retrieval. 
Column of start chromosomal position. 
Column of end chromosomal position. The end column can be the same as the start column. 
Skip first INT lines in the data file. 
Skip lines started with character CHAR. [#]
Specify that the position in the data file is 0-based (e.g. UCSC files) rather than 1-based.
Print the header/meta lines.
The second argument is a BED file. When this option is in use, the input file may not be sorted or indexed. The entire input will be read sequentially. Nonetheless, with this option, the format of the input must be specificed correctly on the command line.
Force to overwrite the index file if it is present.
List the sequence names stored in the index file.
tabix -p gff sorted.gff.gz;
tabix sorted.gff.gz chr1:10,000,000-20,000,000;
Tabix was written by Heng Li. The BGZF library was originally implemented by Bob Handsaker and modified by Heng Li for remote file access and in-memory caching.
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