'\" t .TH samtools-merge 1 "22 September 2020" "samtools-1.11" "Bioinformatics tools" .SH NAME samtools merge \- merges multiple sorted input files into a single output. .\" .\" Copyright (C) 2008-2011, 2013-2019 Genome Research Ltd. .\" Portions copyright (C) 2010, 2011 Broad Institute. .\" .\" Author: Heng Li .\" Author: Joshua C. Randall .\" .\" Permission is hereby granted, free of charge, to any person obtaining a .\" copy of this software and associated documentation files (the "Software"), .\" to deal in the Software without restriction, including without limitation .\" the rights to use, copy, modify, merge, publish, distribute, sublicense, .\" and/or sell copies of the Software, and to permit persons to whom the .\" Software is furnished to do so, subject to the following conditions: .\" .\" The above copyright notice and this permission notice shall be included in .\" all copies or substantial portions of the Software. .\" .\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR .\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, .\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL .\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER .\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING .\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER .\" DEALINGS IN THE SOFTWARE. . .\" For code blocks and examples (cf groff's Ultrix-specific man macros) .de EX . in +\\$1 . nf . ft CR .. .de EE . ft . fi . in .. . .SH SYNOPSIS .PP .B merge samtools merge .RB [ -nur1f ] .RB [ -h .IR inh.sam ] .RB [ -t .IR tag ] .RB [ -R .IR reg ] .RB [ -b .IR list "] " out.bam " " in1.bam " [" in2.bam " " in3.bam " ... " inN.bam ] .SH DESCRIPTION .PP Merge multiple sorted alignment files, producing a single sorted output file that contains all the input records and maintains the existing sort order. If .BR -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 .BR -c or .BR -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 \fB-n\fP and \fB-t\fP command-line options. If they do not, the output order will be undefined. See .B sort for information about record ordering. .TP 8 .B -1 Use Deflate compression level 1 to compress the output. .TP .BI -b \ FILE List of input BAM files, one file per line. .TP .B -f Force to overwrite the output file if present. .TP 8 .BI -h \ FILE Use the lines of .I FILE as `@' headers to be copied to .IR out.bam , replacing any header lines that would otherwise be copied from .IR in1.bam . .RI ( FILE is actually in SAM format, though any alignment records it may contain are ignored.) .TP .B -n The input alignments are sorted by read names rather than by chromosomal coordinates .TP .B -t TAG The input alignments have been sorted by the value of TAG, then by either position or name (if \fB-n\fP is given). .TP .BI -R \ STR Merge files in the specified region indicated by .I STR [null] .TP .B -r Attach an RG tag to each alignment. The tag value is inferred from file names. .TP .B -u Uncompressed BAM output .TP .B -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 \fB-c\fP, all @RG headers appear in the output file, with random suffixes added to their IDs where necessary to differentiate them. .TP .B -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. .TP .B -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 .B EXAMPLES section for sample of usage. .TP .BI -L \ FILE BED file for specifying multiple regions on which the merge will be performed. This option extends the usage of .B -R option and cannot be used concurrently with it. .TP .BI --no-PG Do not add a @PG line to the header of the output file. .TP .BI "-@, --threads " INT Number of input/output compression threads to use in addition to main thread [0]. .SH EXAMPLES .IP o 2 Attach the .B RG tag while merging sorted alignments: .EX 2 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 .EE The value in a .B RG tag is determined by the file name the read is coming from. In this example, in the .IR merged.bam , reads from .I ga.bam will be attached .IR RG:Z:ga , while reads from .I 454.bam will be attached .IR RG:Z:454 . .IP o 2 Include customized index file as a part of arguments: .EX 2 samtools merge [options] -X [ ... ] [ ... ] .EE .SH AUTHOR .PP Written by Heng Li from the Sanger Institute. .SH SEE ALSO .IR samtools (1), .IR samtools-sort (1), .IR sam (5) .PP Samtools website: