1samtools-split(1)            Bioinformatics tools            samtools-split(1)
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NAME

6       samtools split - splits a file by read group.
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SYNOPSIS

9       samtools split [options] merged.sam|merged.bam|merged.cram
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DESCRIPTION

13       Splits  a file by read group, producing one or more output files match‐
14       ing a common prefix (by default based on the input filename) each  con‐
15       taining one read-group.
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17       The  -u  option  may  be  used  to  specify the output filename for any
18       records without an RG tag.
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OPTIONS

22       -u FILE1      Put reads with no RG tag or an unrecognised RG  tag  into
23                     FILE1
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25       -h FILE2      Use  the header from FILE2 when writing the file given in
26                     the -u option.  This header completely replaces  the  one
27                     from  the input file.  It must be compatible with the in‐
28                     put file header, which means it must have the same number
29                     of  references listed in the @SQ lines and the references
30                     must be in the same order and have the same lengths.
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32       -f STRING     Output filename format string (see below) ["%*_%#.%."]
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34       -v            Verbose output
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36       --no-PG       Do not add a @PG line to the header of the output file.
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38       Format string expansions:
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40                        %%   %
41                        %*   basename
42                        %#   @RG index
43                        %!   @RG ID
44                        %.   output format filename extension
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46       -@, --threads INT
47              Number of input/output compression threads to use in addition to
48              main thread [0].
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AUTHOR

52       Written by Martin Pollard from the Sanger Institute.
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SEE ALSO

56       samtools(1), samtools-addreplacerg(1)
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58       Samtools website: <http://www.htslib.org/>
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62samtools-1.13                     7 July 2021                samtools-split(1)
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