bamtools分割bam文件

bam文件可以按照染色体或者tag分割，bam文件的分割可以使用bamtools. 用法：

代码语言：javascript复制

Description: splits a BAM file on user-specified property, creating a new BAM output file for each value found.
Usage: bamtools split [-in <filename>] [-stub <filename stub>] < -mapped | -paired | -reference [-refPrefix <prefix>] | -tag <TAG> >
Input & Output:
  -in <BAM filename>                the input BAM file [stdin]
  -refPrefix <string>               custom prefix for splitting by
                                    references. Currently files end with
                                    REF_<refName>.bam. This option allows you
                                    to replace "REF_" with a prefix of your
                                    choosing.
  -tagPrefix <string>               custom prefix for splitting by
                                    tags. Current files end with
                                    TAG_<tagname>_<tagvalue>.bam. This option
                                    allows you to replace "TAG_" with a prefix
                                    of your choosing.
  -stub <filename stub>             prefix stub for output BAM
                                    files (default behavior is to use input
                                    filename, without .bam extension, as
                                    stub). If input is stdin and no stub
                                    provided, a timestamp is generated as the
                                    stub.
  -tagListDelim <string>            delimiter used to separate
                                    values in the filenames generated from
                                    splitting on list-type tags [--]

Split Options:
  -mapped                           split mapped/unmapped
                                    alignments
  -paired                           split single-end/paired-end
                                    alignments
  -reference                        split alignments by reference
  -tag <tag name>                   splits alignments based on all
                                    values of TAG encountered (i.e. -tag RG
                                    creates a BAM file for each read group in
                                    original BAM file)

简单来说，bamtools split 用法为： -in ：指定输入的需要分割的bam文件 -reference ：按染色体分割 -refPrefix :将按染色体分割生成的文件名字前缀"REF_"替换 -tagPrefix:将按tag分割生成的文件名字前缀"TAG_"替换

1.按染色体分割bam文件

代码语言：javascript复制

bamtools split -in tmp.bam -reference

2.按tag分割bam文件

代码语言：javascript复制

bamtools split -in tmp.bam -tag RG

参考： https://github.com/pezmaster31/bamtools/issues/135

reference split

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