HiNT (Hi-C for copy Number variation and Translocation detection), a computational method to detect CNVs and Translocations from Hi-C data. HiNT has three main components: HiNT-PRE, HiNT-CNV, and HiNT-TL. HiNT-PRE preprocesses Hi-C data and computes the contact matrix, which stores contact frequencies between any two genomic loci; both HiNT-CNV and HiNT-TL starts with HI-C contact matrix, predicts copy number segments, and inter-chromosomal translocations, respectively

https://github.com/parklab/HiNT

• Module Name: hint (see the modules page for more information)
• see /fdb/hint for reference, index, matrices, and example files
• Programs are multithreaded.

Allocate an interactive session and run the interactive job there.

[biowulf]$ sinteractive  --mem=40g  --cpus-per-task=16
salloc.exe: Granted job allocation 789523
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0135 are ready for job

[cn0135]$ cd /data/$USER/

[cn0135]$ module load hint

[cn0135]$ cp /fdb/hint/testData/ . 

[cn0135]$ cd testData

[cn0135]$ hint pre -d $TESTDIR/test.bam \
--refdir $REFDIR/hg19 \
--informat bam \
--outformat juicer \
-g hg19 \
-n test \
-o /data/$USER/out \
--samtoolspath $SAMTOOLS \
-p $SLURM_CPUS_PER_TASK \
--pairtoolspath $PAIRTOOLS \
--juicerpath $JUICERPATH/scripts/juicer_tools_1.22.01.jar
[14:42:34] Argument List:
[14:42:34] Hi-C data = /, f, d, b, /, h, i, n, t, /, t, e, s, t, D, a, t, a, /, t, e, s, t, ., b, a, m
[14:42:34] Input format = bam
[14:42:34] Output format = juicer
[14:42:34] Genome = hg19
...
...
Calculating norms for zoom BP_10000
Calculating norms for zoom BP_5000
Writing expected
Writing norms
Finished writing norms

or

[cn0135]$ hint pre \
-d $TESTDIR/TestSub_1.fq.gz,$TESTDIR/TestSub_2.fq.gz \
-a $BWA \
-i $BWAINDEXDIR/hg19/hg19.fa \
--refdir $REFDIR/hg19 \
--informat fastq \
--outformat cooler \
-g hg19 \
-n test \
-o /data/$USER/out \
--samtoolspath $SAMTOOLS \
-p $SLURM_CPUS_PER_TASK \
--pairtoolspath $PAIRTOOLS \
--coolerpath $COOLER

or

[cn0135]$ hint tl \
-m test.hic \
-f juicer \
--refdir $REFDIR/hg19 \
--backdir $MATRICESDIR/hg19 \
-g hg19 \
-n test \
-c 0.05 \
--ppath $PAIRIX \
-p $SLURM_CPUS_PER_TASK \
-o testout

[cn0135]$ exit
salloc.exe: Job allocation 789523 has been revoked.
[biowulf]$

Note: this job allocates 10 GB of memory and automatically assign the number of cpus allocated to the variable $SLURM_CPUS_PER_TASK.

The test takes less than 30 minutes.

1. Create a script file (myscript) similar to the one below.

#!/bin/bash 

cd /data/$USER/testData
module load hint
hint pre -d $TESTDIR/test.bam \
--refdir $REFDIR/hg19 \
--informat bam \
--outformat juicer \
-g hg19 \
-n test \
-o /data/$USER/out \
--samtoolspath $SAMTOOLS \
-p $SLURM_CPUS_PER_TASK \
--pairtoolspath $PAIRTOOLS \
--juicerpath $JUICERPATH

2. Submit the script on biowulf:

[biowulf]$ sbatch --mem=40g --cpus-per-task=8  myscript

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/$USER/cmdfile).

cd /data/$USER/dir1; hint pre -d $TESTDIR/test.bam ...
cd /data/$USER/dir2; hint pre -d $TESTDIR/test.bam ...
cd /data/$USER/dir3; hint pre -d $TESTDIR/test.bam ...
...
cd /data/$USER/dir20; hint pre -d $TESTDIR/test.bam ...

submit the swarm job:

$ swarm -f cmdfile --module hint -g 40 -t 16

For more information regarding running swarm, see swarm.html