Tumor Heterogeneity Analysis (THetA) is an algorithm used to estimate tumor purity and clonal/subclonal copy number aberrations simultaneously from high-throughput DNA sequencing data.

References:

• L. Oesper, G. Satas, and B.J. Raphael. Quantifying Tumor Heterogeneity in Whole-Genome and Whole-Exome Sequencing Data. Bioinformatics 2014, 30:3532-3540. Pubmed |  PMC |  Journal

• GitHub
• Home page

• Module Name: theta (see the modules page for more information)
• THetA is a multithreaded application. Please match the number of processes with your allocation.
• Example files in /usr/local/apps/theta/TEST_DATA/example

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=14g --cpus-per-task=6
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load theta/0.7-20-g94fd772
[user@cn3144 ~]$ cp -r ${THETA_TEST_DATA:-none}/example/ .
[user@cn3144 ~]$ RunTHetA example/Example.intervals \
                        --NUM_PROCESSES=$((SLURM_CPUS_PER_TASK - 1)) \
                        --TUMOR_FILE example/TUMOR_SNP.formatted.txt \
                        --NORMAL_FILE example/NORMAL_SNP.formatted.txt
=================================================
Arguments are:
        Query File: example/Example.intervals
        k: 3
        tau: 2
        Output Directory: ./
        Output Prefix: Example
        Num Processes: 5
        Graph extension: .pdf

Valid sample for THetA analysis:
        Ratio Deviation: 0.1
        Min Fraction of Genome Aberrated: 0.05
        Program WILL cluster intervals.
=================================================
Reading in query file...
[...snip...]

[user@cn3144 ~]$ ls -lh
total 232K
drwxr-xr-x 2 user group 4.0K Oct 13 10:32 example
drwxr-xr-x 9 user group 4.0K Oct 13 16:19 Example_2_cluster_data
drwxr-xr-x 8 user group 4.0K Oct 13 16:20 Example_3_cluster_data
-rw-r--r-- 1 user group  13K Oct 13 16:19 Example_assignment.png
-rw-r--r-- 1 user group 2.0K Oct 13 16:20 Example.BEST.results
-rw-r--r-- 1 user group 118K Oct 13 16:19 Example_by_chromosome.png
-rw-r--r-- 1 user group  17K Oct 13 16:19 Example_classifications.png
-rw-r--r-- 1 user group  16K Oct 13 16:19 Example.n2.graph.pdf
-rw-r--r-- 1 user group 2.0K Oct 13 16:19 Example.n2.results
-rw-r--r-- 1 user group 3.6K Oct 13 16:19 Example.n2.withBounds
-rw-r--r-- 1 user group  17K Oct 13 16:20 Example.n3.graph.pdf
-rw-r--r-- 1 user group 2.2K Oct 13 16:20 Example.n3.results
-rw-r--r-- 1 user group 3.6K Oct 13 16:20 Example.n3.withBounds
-rw-r--r-- 1 user group  225 Oct 13 16:19 Example.RunN3.bash

The analysis will create a number of files including some graphs. For example, the following shows one of the models (2 components):

In addition to RunTHetA there are several other tools included in this package

[user@cn3144 ~]$ ls /usr/local/apps/theta/0.7-20-g94fd772/bin
|-- CreateExomeInput
|-- getAlleleCounts
|-- runBICSeqToTHetA
`-- RunTHetA

2 of these tools (getAlleleCounts and runBICSeqToTHetA) are wrappers around java tools. In addition to their normal arguments they also take the --java-opts argument which can be used to pass options to java

[user@cn3144 ~]$ runBICSeqToTHetA --java-opts="-Xmx2g" --help
Error! Incorrect number of arguments.

Program: BICSeqToTHetA
USAGE (src): java BICSeqToTHetA <INPUT_FILE> [Options]
USAGE (jar): java -jar BICSeqToTHetA <INPUT_FILE> [Options]
<INPUT_FILE> [String]
         A file output by BIC-Seq.
-OUTPUT_PREFIX [STRING]
         Prefix for all output files.
-MIN_LENGTH [Integer]
         The minimum length of intervals to keep.

For a more detailed manual see

/usr/local/apps/theta/<version>/MANUAL.txt

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. THetA.sh), which uses the input file 'THetA.in'. For example:

#! /bin/bash
module load theta/0.7-20-g94fd772 || exit 1

RunTHetA example/Example.intervals \
  --NUM_PROCESSES=$((SLURM_CPUS_PER_TASK - 1)) \
  --TUMOR_FILE example/TUMOR_SNP.formatted.txt \
  --NORMAL_FILE example/NORMAL_SNP.formatted.txt

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=14g theta.sh

Create a swarmfile (e.g. THetA.swarm). For example:

RunTHetA sample1/Example.intervals --NUM_PROCESSES=$((SLURM_CPUS_PER_TASK-1)) \
  --TUMOR_FILE sample1/TUMOR_SNP.formatted.txt --NORMAL_FILE sample2/NORMAL_SNP.formatted.txt
RunTHetA sample2/Example.intervals --NUM_PROCESSES=$((SLURM_CPUS_PER_TASK-1)) \
  --TUMOR_FILE sample2/TUMOR_SNP.formatted.txt --NORMAL_FILE sample2/NORMAL_SNP.formatted.txt

Submit this job using the swarm command.

swarm -f THetA.swarm -g 14 -t 6 --module theta