Class: Bio::Ngs::Samtools::Merge

Inherits:

Object

• Object
• Bio::Ngs::Samtools::Merge

Includes:

Command::Wrapper

Defined in:

lib/bio/appl/ngs/samtools.rb

Overview

Usage: samtools merge [-nr] [-h inh.sam] <out.bam> <in1.bam> <in2.bam> […]

Options: -n sort by read names

-r       attach RG tag (inferred from file names)
-u       uncompressed BAM output
-f       overwrite the output BAM if exist
-1       compress level 1
-R STR   merge file in the specified region STR [all]
-h FILE  copy the header in FILE to <out.bam> [in1.bam]

Note: Samtools’ merge does not reconstruct the @RG dictionary in the header. Users

must provide the correct header with -h, or uses Picard which properly maintains
the header dictionary in merging.

out, in1, in2, … inx Must be passed as arguments

Method Summary

Methods included from Command::Wrapper

#class_name, #default_options, included, #initialize, #normalize_params, #options, #options=, #output, #params, #params=, #path, #path=, #pipe_ahead, #pipe_ahead=, #pipe_ahead?, #program, #reset_params, #run, #sub_program, #thor_task, #to_cmd_ary, #use_aliases?