samtools-split - splits a file by read group.
samtools split [
options]
merged.sam|
merged.bam|
merged.cram
Splits a file by read group, producing one or more output files matching a
common prefix (by default based on the input filename) each containing one
read-group.
The
-u option may be used to specify the output filename for any records
without an RG tag.
-
-u FILE1
- Put reads with no RG tag or an unrecognised RG tag into
FILE1
-
-h FILE2
- Use the header from FILE2 when writing the file
given in the -u option. This header completely replaces the one
from the input file. It must be compatible with the input file header,
which means it must have the same number of references listed in the @SQ
lines and the references must be in the same order and have the same
lengths.
-
-f STRING
- Output filename format string (see below)
["%*_%#.%."]
- -v
- Verbose output
- --no-PG
- Do not add a @PG line to the header of the output
file.
Format string expansions:
| %% |
% |
| %* |
basename |
| %# |
@RG index |
| %! |
@RG ID |
| %. |
output format filename extension |
-
-@, --threads INT
- Number of input/output compression threads to use in
addition to main thread [0].
Written by Martin Pollard from the Sanger Institute.
samtools(1),
samtools-addreplacerg(1)
Samtools website: <
http://www.htslib.org/>