A new method, PhyloWGS, can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations.

References:

• Amit G Deshwar, Shankar Vembu, Christina K Yung, Gun Ho Jang, Lincoln Stein and Quaid Morris. PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome Biology 2015 16:35

• Phylowgs Main Site

• Module Name: phylowgs (see the modules page for more information)
• Singlethreaded app
• Phylowgs results can be viewed in local browser using SSH Tunneling
• Example files in /usr/local/apps/phylowgs/TEST_DATA

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

[user@biowulf]$ sinteractive --gres=lscratch:20 
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 ~]$ mkdir -p /data/$USER/phylowgs && cd /data/$USER/phylowgs

[user@cn3144 ~]$ module load phylowgs

[user@cn3144 ~]$ cp /usr/local/apps/phylowgs/TEST_DATA/* .

[user@cn3144 ~]$ evolve.py ssm_data.txt cnv_data.txt -t /lscratch/$SLURM_JOBID
[2018-02-16 09:19:38.999007] Starting MCMC run...
[2018-02-16 09:19:39.004639] -1000
[2018-02-16 09:19:39.301332] Shrinking MH proposals. Now 200.000000
[2018-02-16 09:19:39.311407] -999
[2018-02-16 09:19:39.646055] Shrinking MH proposals. Now 400.000000
[2018-02-16 09:19:39.652818] -998
...

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

Create a batch input file (e.g. phylowgs.sh). For example:

#!/bin/bash
set -e
module load phylowgs
evolve.py ssm_data.txt cnv_data.txt -t /lscratch/$SLURM_JOBID

Submit this job using the Slurm sbatch command.

sbatch --gres=lscratch:20 phylowgs.sh

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

evolve.py dir1/ssm_data1.txt dir1/cnv_data1.txt -t /lscratch/$SLURM_JOBID
evolve.py dir2/ssm_data2.txt dir2/cnv_data2.txt -t /lscratch/$SLURM_JOBID
evolve.py dir3/ssm_data3.txt dir3/cnv_data3.txt -t /lscratch/$SLURM_JOBID

Submit this job using the swarm command.

swarm -f phylowgs.swarm --gres=lscratch:20 -g 5 -t 2 --module phylowgs