Pascal

This package hooks into the jrflab/modules sequencing pipeline for tailored / dynamic analysis.

Setup

From root project directory:

1. initialize with: sh pascal/init.sh
2. build subsets file by editing the subsets.txt file as follows (space delimited):

subsetName1 sample1 sample2
subsetName2 sample1 sample3 sample4

subsetRecurrence

Builds a prevelance-ordered, subsetted heatmap + table of recurrent mutations from the master recurrent mutation table.

Prerequisites

• requires: make recurrent_mutations
• working installation of sufam

Run

Rscript pascal/recurrence/subsetRecurrence.R

Generates heatmap .pdf and table files in recurrent_mutations directory within project root.

sufamRecurrent

Performs base-truth recurrent mutation lookups in the .bam files of all samples within subsets.

Prerequisites

• requires: make recurrent_mutations

Run

Rscript pascal/recurrence/sufamRecurrent.R

Generates log file in log directory, vcf and sufam output .tsv in recurrent_mutations directory

sufamEventSearch

Use Sufam to arbitrarily search for base-truth genomic events in a sample subset by specifying a vcf file.

Prerequisites

• add genomic positions of interest to events.vcf, column headings required #CHROM POS ID REF ALT
• will run on all samples found in subsets.txt

Run

Rscript pascal/recurrence/sufamEventSearch.R

PyClone

Prerequisites

• make mutation_summary
• make facets
• will run on all samples found in subsets.txt

Run

Rscript pascal/clonality/pyclone.R

PhyloWGS

EXPANDS

SCHISM