A tool to extract subsets of data from the tagged BAM file generated by CellRanger
You can clone this repository but will need to do
pip install pysam
to get it working. Since pysam only works on linux (not windows) then this tool will only work there too.
$ ./subset10bam --help
usage: subset10bam [-h] [--quiet] [--version] [--outdir OUTDIR]
[--threads THREADS] [--force FORCE]
bamfile cellids
Extract read subsets from CellRanger BAM files
positional arguments:
bamfile A CellRanger BAM file
cellids A text file list of Cell Barcodes to extract
optional arguments:
-h, --help show this help message and exit
--quiet Supress all but essential messages
--version show program's version number and exit
--outdir OUTDIR Folder to save data to (default .)
--threads THREADS Number of threads (default 1)
--add_barcode Add cell barcode (tag CB:Z:) to readID
--force Overwrite output files even if they exist