Single-cell Variant Calling via Integer Linear Programming (scVILP)

single-cell Variant-calling by Integer Linear Programming (scVILP) is a new approach to mutation calling in single cells with Perfect Phylogeny assumption using Integer Linear Programming formulations. scVILP jointly calls mutations for each cell and estimates the Perfect Phylogeny of those cells in the presence of allelic dropouts and missing data. It is possible for the user to investigate the violations of infinite-sites assumption on the inference by setting an upper bound on the number of violations

Contents

• Getting started
  • Prerequisites
• Required inputs
• Running scVILP
  • Identify the candidate loci
  • Run the variant caller
• Outputs
• Contact

Getting started

Prerequisites

• Anaconda - we recommend installing Anaconda for your OS to manage the required packages
• Gurobi - after installation of Anaconda, you need to install Gurobi optimizer into Anaconda for Integer Linear Programming
• PerfectPhy - to reconstruct the Perfect Phylogeny we have used PerfectPhy package. You can download it from here or install the version provided in the scripts directory of this repository
• ete3 - install Python package, ete3 into Anaconda by running:

  conda install -c etetoolkit ete3

• PAUP - to visualize the phylogenetic tree using the Newick output file, download and install PAUP

Required inputs

• The input data of scVILP is the output of sequence alignment in mpileup format
• At least the number of cells is required, or a file containing the cell names which is optional, in case the cell names are not avaialble, they are named as cell k where k is the index of the cell

Running scVILP

Identify the candidate loci

First, run one of the following commmands to identify the candidate mutation loci 1- With the number of cells:

python loci_identify.py -in ovarian.mpileup -out ./output.mpileup -n 370 -ms 2 -nmc 3 

2- Or, using a text file containing the cell names to run this code:

python loci_identify.py -in ovarian.mpileup -out ./output,mpileup -names cellNames.txt -ms 2 -nmc 3

At this step, the user needs to select the loci on which they are performing the analysis. The parameters are as follows:

• in: path to the input file
• out: path to the output file
• ms: at each cell and genomic loci, this parameter requires a minimum of ms variant counts
• nmc: at each genomic loci, this parameter requires at least n cells to have the minimum number of variants (m)

Run the variant caller

To run the optimizer, enter the following command:

python scVILP_main.py -in <path to the mpileup file> -names <path to the cell names> -out <path to the output directory>

To see the other options:

python scVILP_main.py --help

Outputs

Running the main code, generates two files in the output directory specified by the user:

• A VCF file named snv.vcf describing the inferred genotypes for all the cells
• A Nexus file named phylogeny.nex containing the Newick string of the Perfect Phylogeny with leaves labeled by cell names
  • Note: Our method generates the phylogenetic tree in Newick format only when there is no violations of infinite-sites assumption. Before running scVILP, please specify the path to the directory of PerfectPhy in scVILP_main.py, the default path to PerfectPhy directory is the same where the scripts are.

Contact

Please feel free to contact edrisi@rice.edu if you have any questions