samtools-merge - Man Page

samtools merge [options] -o out.bam [options] in1.bam ... inN.bam

samtools merge [options] out.bam in1.bam ... inN.bam

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

The output file can be specified via -o as shown in the first synopsis. Otherwise the first non-option filename argument is taken to be out.bam rather than an input file, as in the second synopsis. There is no default; to write to standard output (or to a pipe), use either “-o -” or the equivalent using “-” as the first filename argument.

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

-o FILE

Write merged output to FILE, specifying the filename via an option rather than as the first filename argument. When -o is used, all non-option filename arguments specify input files to be merged.

-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 usage.

-L FILE

BED file for specifying multiple regions on which the merge will be performed. This option extends the usage of -R option and cannot be used concurrently with it.

--no-PG

Do not add a @PG line to the header of the output file.

-@,  --threads INT

Number of input/output compression threads to use in addition to main thread [0].

• 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.

• Include customized index file as a part of arguments:

  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>]

Written by Heng Li from the Sanger Institute.

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

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

samtools(1), samtools-sort(1).