MonovarNG is a single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data. It takes a list of bam files as input and outputs a vcf file containing the detected SNVs. This improved version of Monovar is written in C++ and achieves 3600x speedup over the original Monovar. The accuracy is also improved
Install dependencies
sudo apt-get install git g++ cmake libboost-all-dev zlib1g-dev libbz2-dev liblzma-dev lbzip2
Install htslib
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
tar -xvf htslib-1.9.tar.bz2
cd htslib-1.9
./configure
make
sudo make install
Build Monovar
git clone https://github.com/tianyi5309/MonovarNG
cd MonovarNG
cmake .
make
Add Monovar to path
export PATH=$PATH:$PWD/bin/
The program requires multiple bam files. The bam files should be sorted by coordinates. The raw sequence reads in .fastq format should be aligned to a reference genome with the help of an aligner program (e.g., BWA (http://bio-bwa.sourceforge.net/)). Aligner like BWA generates sam files containing aligned reads. The sam files can be converted to compressed bam files using samtools view command (see Samtools manual for details http://www.htslib.org/doc/samtools.html).
monovar ref.fa filenames.txt compiled.pl output.vcf [-patm]
The arguments of Monovar are as follows:
-t: Threshold to be used for variant calling (Recommended value: 0.05)
-p: Offset for prior probability for false-positive error (Recommended value: 0.002)
-a: Offset for prior probability for allelic drop out (Default value: 0.2)
-m: Number of threads to use in multiprocessing (Default value: 1)
We recommend using cutoff 40 for mapping quality when using samtools mpileup. To use the probabilistic realignment for the computation of Base Alignment Quality, drop the -B while running samtools mpileup.