MutSig

A slim tool for counting the mutational signature from a VCF file.

Usage

Count number of single-nucleotide-variations in a single- or multi-sample VCF file:

mutsig my_sample.vcf.gz reference_genome.fa.gz > singlets.txt

The output will be a simple matrix in tab-separated text format containing the variant in the first column followed by the samples in the following columns.

To count single-nucleotide variations in triplets, specify the window-size (i.e., number of bases up- and downstream to consider).

mutsig my_sample.vcf.gz reference_genome.fa.gz -w 1 > triplets.txt

If you have a multi-sample VCF you may want to ignore the position which are homogeneous in all samples:

mutsig my_sample.vcf.gz reference_genome.fa.gz -i > non_homogeneous_singlets.txt

Installation

Cargo

If you have the Rust toolchain installed, it is as simple as

cargo install

Conda

Planned

Author