mutationProfiles

This is a tool to extract and analyse SNV information from VCF files produced by Mutect2 or Varscan2.
This tool is under constant development. Please feel free to contact me, or raise an issue if you encounter any problems.

Installation

Install from github:

git clone https://github.com/nriddiford/mutationProfiles.git
cd mutationProfiles

Dependencies

trinucs.pl requires BioPerl, which can be installed using cpanm:

brew install cpanm
sudo cpanm Bio::Perl

and vcfParse, which can be installed from github:

git clone https://github.com/nriddiford/vcfParse.git
cd vcfParse
perl Makefile.PL
make
make test
make install

Extracting SNV calls from Mutect2 or Freebayes vcf files or Varscan2 native format

Move all .vcf files into data/ and run bash run_trinucs.sh -g <path to genome.fasta>
For Varscan native data run: bash run_trinucs.sh -v -g <path to genome.fasta>

This will run script/trinucs.pl on each .vcf file in data/, and write data from all samples to data/combined_snvs.txt in the following format:

[sample] [chrom] [pos] [ref] [alt] [tri context] [ref>alt] [decomposed trinuc context] [decomposed ref>alt] [type]

A512R17    2L    229832    A    C    CAG    A>C    CTG    T>G    somatic
A512R17    2L    1819239    T    A    TTC    T>A    TTC    T>A    somatic
A512R17    2L    2439881    C    T    GCC    C>T    GCC    C>T    somatic
A512R17    2L    3154318    C    G    GCC    C>G    GCC    C>G    somatic
A512R17    2L    3511198    G    A    CGA    G>A    TCG    C>T    somatic
A512R17    2L    4565784    C    G    CCT    C>G    CCT    C>G    somatic
A512R17    2L    5233457    T    G    TTA    T>G    TTA    T>G    somatic
A512R17    2L    6478473    G    C    GGT    G>C    ACC    C>G    somatic
A512R17    2L    9792284    C    T    GCC    C>T    GCC    C>T    somatic

Annotate SNVs with gene and feature it’s contained within

Run perl script/snv2gene.pl -i data/combined_snvs.txt to annotate the gene and feature hit by each SNV

e.g.:

[sample] [chrom] [pos] [ref] [alt] [tri context] [ref>alt] [decomposed trinuc context] [decomposed ref>alt] [type] [feature] [gene]

A512R17 2L      229832  A       C       CAG     A>C     CTG     T>G     somatic intron  kis
A512R17 2L      1819239 T       A       TTC     T>A     TTC     T>A     somatic intergenic      intergenic
A512R17 2L      2439881 C       T       GCC     C>T     GCC     C>T     somatic intron  dpp
A512R17 2L      3154318 C       G       GCC     C>G     GCC     C>G     somatic intron  Mad
A512R17 2L      3511198 G       A       CGA     G>A     TCG     C>T     somatic exon_5  LeuRS
A512R17 2L      4565784 C       G       CCT     C>G     CCT     C>G     somatic intron  dpy
A512R17 2L      5233457 T       G       TTA     T>G     TTA     T>G     somatic intron  tkv

Explore snv data

Start an R session, and install package:

library(devtools)
install_github("nriddiford/mutationProfiles")
library(mutationProfiles)
setwd('mutationProfiles')

mutationProfiles

The following functions are included:

chromDist : function (object = NA, notch = 0)
cleanTheme : function (base_size = 12)
featuresHit : function ()
geneHit : function (n = 10)
genomeSnvs : function ()
genTris : function ()
getData : function (infile = "data/annotated_snvs.txt")
mutSigs : function (samples = NA, pie = NA)
mutSpectrum : function ()
notchSnvs : function ()
samplesPlot : function (count = NA)
setCols : function (df, col)
snvStats : function ()
triFreq : function (genome = NA, count = NA)

See some stats

snvStats()

Plot mutations per sample

samplesPlot()

Plot mutation spectrum for all samples combined

mutSpectrum()

Plot mutational signatures in data

This plots the output of the package deconstructSigs

mutSigs()

Plot distribution of snvs across chromosomes

chromDist()

Plot number of times a feature type has been hit_ref

featuresHit()

Show the 20 most hit genes

geneHit(n=20)