Ngs MergeNgsFiles.pdf

From Array Suite Wiki

Merge Files

The Merge Data command is used to merge multiple NGS files into one file, or by a group. This can be useful if the NGS files were previously split by chromosome or some other factor. This command will also allow the user to quickly concatenate multiple gzipped files into a standard gzipped file.

Ngs MergeFiles Menu.png

File formats for input include "Binary sequence Alignment/Mapping" (BAM), "Sequence Alignment/Mapping" (SAM) formats, and RAW ( fastq, fasta, txt , gz or any other type of file).

Upon select the "Merge" command, the following window appears:



The Merge options

  • Merge all files into one file.
  • Merge files by group. If the user chooses merge files by group, they need to specify a grouping file containing two columns (first column is the input file’s full path and the second column is the group).
  • If the input files are already sorted by genomic coordinates, the user can check this option and the output files will also be sorted by genomic coordinates.


  • Output file formats include BAM or SAM.
  • Output file prefix - If specified, will add a prefix to each of the output files.
  • Output folder - To specify the location of the output files.