SCARLET

SCARLET is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.

SCARLET is implemented in Python and uses Gurobi for optimization.

Contents

1. Setup
   • Dependencies
   • Using Gurobi
2. Running SCARLET
   • Input
   • Output
   • Usage
3. Example

Setup

Dependencies

• Python 2.7 Python 3 since last commit (anaconda distribution recommended)
• Gurobi
• GraphViz (for tree visualization)

SCARLET Setup

To use SCARLET, first clone the SCARLET repository locally.

git clone git@github.com:raphael-group/scarlet.git

SCARLET uses Python and doesn't require any compilation. SCARLET does however require an installation and a valid lincense for the Gurobi Optimizier. See the following section for details.

Using Gurobi

SCARLET uses the Gurobi optimizer. To setup Gurobi, first download the Gurobi Optimizer.

Every run of SCARLET uses Gurobi, which requires a valid license pointed to by the enviromental variable GRB_LICENSE_FILE. Gurobi licenses are freely available for academic users and can be acquired at https://www.gurobi.com/academia/. There are two types of academic licenses available:

1. Individual license. This license can be obtained easily by any academic user with an institutional email. This license is user and machine-specific, meaning that the user needs to acquire a different license for every machine. Assuming the license is stored at /path/to/gurobi.lic, the user can easily use it by the following command:

   export GRB_LICENSE_FILE="/path/to/gurobi.lic"

2. Multi-user license. This license can be used by multiple users on any machine in a cluster. This license can be obtained freely but needs to be requested by the IT staff of the user's institution. This license is typically used in a machine cluster and requires the following command:

   module load gurobi

Running SCARLET

Input Files

SCARLET takes as input two files. The first describes the read counts and copy-number profile assignments for each cell. The second describes the copy-number tree and the set of supported losses for each edge in the copy-number tree.

1. Read count file. For each cell, this file describes the copy-number profile assignment and variant and total read counts for m mutations. The input file is a comma-separated file, where the first line is the header and rows correspond to cells, with the following format.

   cell_id, c, [mut1]_v, [mut1]_t, [mut2]_v, [mut2]_t, ... [mutm]_v, [mutm]_t
   
   

   • cell_id --- unique identifier for each cell
   • c --- [non-negative integer] copy-number profile assignment
   • [muti_v] --- [non-negative integer] the variant read count for mutation i in a particular cell
   • [muti_t] --- [non-negative integer] the integer total read count for mutation i in a particular cell. By definition, the total read count must be greater than or equal to the variant read count.

   Note that in the header [muti] may be replaced with unique identifiers for mutations, but the rest of the format must remain as specified.

2. Copy-number tree file. This file describes the copy-number tree that relates the copy-number profiles of the observed leaves, as well as the set of supported losses for each copy-number transition. This file takes the format of an comma-separated edge list, where the first two columns are integer copy-number profiles, followed by a list of supported losses on that transition.

   c_1, c_2, [mut1], [mut3], ..., [muti]
   c_2, c_3, [mut2], [mut5], ..., [mutj]
   

   Copy-number profile assignments and mutation names must be consistent with those found in the read count file.

Examples of these files can be found in the example/ directory.

Output Files

Scarlet produces several output files, as detailed below. In addition to these, Scarlet produces several auxiliary files (including [prefix].B_ancestor and [prefix].dot) that are used for graphing purposes and not detailed below.

1. Binary mutation matrix file ([prefix].B). This file describes the binary presence (1) or absence (0) of each mutation in each cell. This is a comma-separated file where the first line is the header and rows correspond to cells, of the following format.

   cell_id,[mut1], [mut2], ..., [mutm]
   
   

2. Ternary mutation matrix file ([prefix].T). This file is formated in the same way as the binary mutation matrix file but also indicates mutation losses (2). That is, if an ancestor of a cell contained a mutation but it was subsequently lost, the mutation matrix entry for that cell will be a 2 instead of a 0.

3. Mutation matrix likelihood file ([prefix].LL). This file contains a single line which gives the log-likelihood of the mutation matrix.

4. Tree edgelist ([prefix].edgelist). This file contains a list of edges in the tree inferred by SCARLET. In this file, there are three types of vertices. Observed cells are prefixed by "CELL:" and labeled by their id (as given in the read count file). Internal vertices that correspond to the roots of a copy-number state subtree are prefixed by "ROOT:", and labeled by the copy-number state. Internal vertices are prefixed by "MUT:" and labeled by the mutation on the incoming edge to that vertex. All vertex names are followed by the assigned copy-number state in parenthesis.

Usage

SCARLET can be run from the command line as follows.

bash code/scarlet.sh [read count file] [copy-number tree file] [output prefix] [(OPTIONAL) plotting_style]

Plotting style controls how the leaves will be displayed in the plot of the output tree. It has three options.

• "ALL": Plot all observed cells as leaves

• "COUNT": Plot the number of observed cells attached to each inner vertex

• "NONE": Plot only the mutation tree, no leaves

Example

Example input is provided in the example directory. It can be run as

bash code/scarlet.sh example/read_counts.csv example/tree.csv example/output ALL