Manual page from samtools-1.20
released on 15 April 2024


samtools merge – merges multiple sorted files into a single file


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, -N and -t command-line options. If they do not, the output order will be undefined. Note this also extends to disallowing mixing of "queryname" files with a combination of natural and lexicographical sort orders. See sort for information about record ordering.

Problems may arise when attempting to merge thousands of files together. The operating system may impose a limit on the maximum number of simultaneously open files. See ulimit -n for more information. Additionally many files being read from simultaneously may cause a certain amount of "disk thrashing". To partially alleviate this the merge command will load 1MB of data at a time from each file, but this in turn adds to the overall merge program memory usage. Please take this into account when setting memory limits.

In extreme cases, it may be necessary to reduce the problem to fewer files by successively merging subsets before a second round of merging.


Use Deflate compression level 1 to compress the output.


List of input BAM files, one file per line.


Force to overwrite the output file if present.


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.)


The input alignments are sorted by read names using an alpha-numeric ordering, rather than by chromosomal coordinates. The alpha-numeric or “natural” sort order detects runs of digits in the strings and sorts these numerically. Hence "a7b" appears before "a12b". Note this is not suitable where hexadecimal values are in use.


The input alignments are sorted by read names using a lexicographical ordering, rather than by chromosomal coordinates. Unlike -n no detection of numeric components is used, instead relying purely on the ASCII value of each character. Hence "x12" comes before "x7" as "1" is before "7" in ASCII. This is a more appropriate name sort order where all digits in names are already zero-padded and/or hexadecimal values are being used.


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).


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


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


Uncompressed BAM output


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.


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.


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.


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.


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].



Written by Heng Li from the Sanger Institute.


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

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