Option or wrapper script for automatic .bam split, per cluster, based on the default cell ranger clustering results and output folder structure?

[vertesy]

First off, thanks for sharing this tool, its really great! I understand that it is "not officially supported", but since you were willing to share it, I thought you might help out with a problem that I am sure you solved already in house.

Does this script have an option, or do you have a wrapper script to automatically split the /outs/possorted_genome_bam.bam based on the clustering results from Cell Ranger /outs/analysis/clustering/kmeans_6_clusters/clusters.csv assuming the default output folder structure of Cell Ranger?

The clustering results are stored as:

...while (as I understand) the split-bam requires a simple list of cell barcodes for one cluster, then execute it for multiple clusters.

Thanks!

Abel