NAME

       samtools merge - merges multiple sorted input files into a single output.

SYNOPSIS

       merge  samtools  merge  [-nur1f]  [-h inh.sam] [-t tag] [-R reg] [-b list] out.bam in1.bam
       [in2.bam in3.bam ... inN.bam]

DESCRIPTION

       Merge multiple sorted alignment files, producing a single sorted output file that contains
       all the input records and maintains the existing sort order.

       If  -h  is  specified  the  @SQ  headers  of input files will be merged into the specified
       header, otherwise they will be merged into a  composite  header  created  from  the  input
       headers.   If  in  the  process  of merging @SQ lines for coordinate sorted input files, a
       conflict arises as to the order (for example input1.bam has @SQ for a,b,c  and  input2.bam
       has  b,a,c)  then the resulting output file will need to be re-sorted back into coordinate
       order.

       Unless the -c or -p flags are specified then when merging @RG and  @PG  records  into  the
       output  header  then  any  IDs found to be duplicates of existing IDs in the output header
       will have a suffix appended to them to differentiate them from similar header records from
       other files and the read records will be updated to reflect this.

       The  ordering  of  the  records  in  the input files must match the usage of the -n and -t
       command-line options.  If they do not, the output order will be undefined.  See  sort  for
       information about record ordering.

       -1      Use Deflate compression level 1 to compress the output.

       -b FILE List of input BAM files, one file per line.

       -f      Force to overwrite the output file if present.

       -h FILE Use the lines of FILE as `@' headers to be copied to out.bam, replacing any header
               lines that would otherwise be copied from  in1.bam.   (FILE  is  actually  in  SAM
               format, though any alignment records it may contain are ignored.)

       -n      The  input  alignments  are  sorted  by  read  names  rather  than  by chromosomal
               coordinates

       -t TAG  The input alignments have been sorted by the value of TAG, then by either position
               or name (if -n is given).

       -R STR  Merge files in the specified region indicated by STR [null]

       -r      Attach an RG tag to each alignment. The tag value is inferred from file names.

       -u      Uncompressed BAM output

       -c      When  several  input  files contain @RG headers with the same ID, emit only one of
               them (namely, the header line from the first file we  find  that  ID  in)  to  the
               merged output file.  Combining these similar headers is usually the right thing to
               do when the files being merged originated from the same file.

               Without -c, all @RG headers appear in the output file, with random suffixes  added
               to their IDs where necessary to differentiate them.

       -p      Similarly,  for  each @PG ID in the set of files to merge, use the @PG line of the
               first file we find that ID in rather than adding a suffix to differentiate similar
               IDs.

       -X      If  this  option  is  set,  it  will  allows user to specify customized index file
               location(s) if the data folder does not  contain  any  index  file.  See  EXAMPLES
               section for sample of useage.

       --no-PG Do not add a @PG line to the header of the output file.

EXAMPLES

       o Attach the RG tag while merging sorted alignments:

           perl -e 'print "@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illumina\n@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt
           samtools merge -rh rg.txt merged.bam ga.bam 454.bam

         The  value  in  a RG tag is determined by the file name the read is coming from. In this
         example, in the merged.bam, reads from ga.bam will be attached RG:Z:ga, while reads from
         454.bam will be attached RG:Z:454.

       o Include customized index file as a part of arugments:

           samtools merge [options] -X <out.bam> </data_folder/in1.bam> [</data_folder/in2.bam> ... </data_folder/inN.bam>] </index_folder/index1.bai> [</index_folder/index2.bai> ... </index_folder/indexN.bai>]

AUTHOR

       Written by Heng Li from the Sanger Institute.

SEE ALSO

       samtools(1), samtools-sort(1), sam(5)

       Samtools website: <http://www.htslib.org/>