三級分析 / bgzip & tabix
===
###### tags: `基因體/三級分析`
###### tags: `生物資訊`, `基因體`, `三級分析`

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[TOC]

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## 安裝
> 安裝 tabix 時，bgzip 也會一併安裝
>

$ apt install tabix

$ tabix
tabix

Version: 1.10.2-3ubuntu0.1
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
   

$ bgzip

Version: 1.10.2-3ubuntu0.1
Usage:   bgzip [OPTIONS] [FILE] ...
Options:
   -b, --offset INT           decompress at virtual file pointer (0-based uncompressed offset)
   -c, --stdout               write on standard output, keep original files unchanged
   -d, --decompress           decompress
   -f, --force                overwrite files without asking
   -h, --help                 give this help
   -i, --index                compress and create BGZF index
   -I, --index-name FILE      name of BGZF index file [file.gz.gzi]
   -l, --compress-level INT   Compression level to use when compressing; 0 to 9, or -1 for default [-1]
   -r, --reindex              (re)index compressed file
   -g, --rebgzip              use an index file to bgzip a file
   -s, --size INT             decompress INT bytes (uncompressed size)
   -@, --threads INT          number of compression threads to use [1]
   -t, --test                 test integrity of compressed file

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## 執行範例

$ bgzip -c file.vcf > file.vcf.gz
$ tabix -p vcf file.vcf.gz