10x Genomics
Chromium Single Cell CNV
Cell Ranger DNA1.0, printed on 10/15/2024
Cell Ranger DNA Algorithms Overview
The algorithms in the cellranger-dna cnv pipeline take as input
- Paired-end sequencing reads from a Chromium Single cell CNV library
- A reference genome
and produces as output
- Copy number calls for each cell
- A hierarchical clustering of cells based on mutual similarity
- Copy number calls for each group of cells defined by the hierarchical clustering
The algorithms can be organized into:
- Preprocessing
- Strip the 10x barcode from each read pair
- Align the reads to the reference genome
- Identify barcodes that correspond to cells
- Compute a coverage profile matrix for each cell at 20 kilobase (kb) genome resolution
- Determine the mappable regions of the genome by simulation
- Single cell copy number calling
- Estimate the copy number for each cell over the mappable regions of the genome
- Impute copy number values over the non-mappable regions
- Clustering
- Build a hierarchical clustering of cells using the single cell copy number calls
- Construct a read coverage profile matrix for each group of cells defined by the hierarchical clustering
- Determine the copy number for each group of cells defined above