Cell Ranger DNA1.1 (latest), printed on 02/09/2023
The cellranger-dna bamslice command filters the position-sorted BAM file produced by a cellranger-dna cnv run to a subset of cells specified with a custom configuration CSV.
These are the most common command line arguments (run cellranger-dna bamslice --help for a full list):
| Argument | Description |
|---|---|
--id=ID | A unique run ID string: e.g. tumor_primary_subset1 |
--csv=CSV | Path of CSV file containing barcode subset definitions (see Configuration). |
--bam=BAM | Path of BAM file to filter (an output of cellranger-dna cnv). |
After specifying these input arguments, run cellranger-dna bamslice. In this example, we're filtering the outputs of a mixed tumor sample:
$ cd /home/jdoe/runs
$ ls -1 tumor_mixed/outs/*.bam # verify the input file exists
tumor_mixed/outs/possorted_bam.bam
$ cellranger-dna bamslice --id=tumor_subsets \
--csv=tumor_subsets.csv \
--bam=/home/jdoe/runs/tumor_mixed/outs/possorted_bam.bam
The pipeline will begin to run, creating a new folder named with the ID you specified (e.g. /home/jdoe/runs/tumor_subsets) for its output. If this folder already exists, cellranger-dna will assume it is an existing pipestance and attempt to resume running it.
A successful run should conclude with a message similar to this:
2019-05-07 10:20:51 [runtime] (chunks_complete) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM 2019-05-07 10:20:51 [runtime] (run:local) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM.fork0.join 2019-05-07 10:20:53 [runtime] (join_complete) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM Outputs: - subsets: /home/jdoe/runs/tumor_subsets/outs/subsets Pipestance completed successfully!
$ ls -1 tumor_subsets/outs/subsets/*.bam normal.bam tumor_primary.bam
Refer to the BAM page for a description of the output BAM files.
You select your barcodes of interest for each group directly, using a separate barcodes file for each group.
A text editor or Excel may be used to construct the configuration CSV. Your spreadsheet may look something like this:
| A | B | |
|---|---|---|
| 1 | library_id | barcodes_csv |
| 2 | normal | /home/jdoe/normal_barcodes.csv |
| 3 | tumor_primary | /home/jdoe/tumor_primary_barcodes.csv |
When you save this to CSV, it will look something like this:
library_id,barcodes_csv normal,/home/jdoe/normal_barcodes.csv tumor_primary,/home/jdoe/tumor_primary_barcodes.csv
The barcodes CSV files will each have one barcode entry per line, including the GEM well suffix (see GEM wells). Each such file will look something like:
AAACGGGTCAAAGTGA-1 AAAGATGCAATGGGAC-1 ... TTTGTCATCCGCACGA-1