Biowulf High Performance Computing at the NIH
WISExome: a within-sample comparison approach to detect copy number variations

Sequence reads obtained with the Whole Exome Sequencing (WES) vary between samples, complicating accurate CNV detection with WES. WISExome is the tool that implements a within-sample comparison approach to CNV detection. It correctly identifies known pathogenic CNVs.

References:

Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive --mem=8g
[user@@cn3316 ~]$ module load WISExome 
[user@@cn3316 ~]$ git clone https://github.com/VUmcCGP/wisexome.git
[user@@cn3316 ~]$ cd wisexome
[user@@cn3316 ~]$ sed -i 's/sys.stderr.write/# sys.stderr.write/g' test.py
[user@@cn3316 ~]$ cp $WEXOME_BIN/*.sh . 
1) Get sample data:
[user@@cn3316 ~]$  ln -s /fdb/WISExome/WISExome_SRR1273288.bam
[user@@cn3316 ~]$  ln -s /fdb/WISExome/ucscrefseq.bed
[user@@cn3316 ~]$  ln -s /fdb/WISExome/SeqCap_EZ_Exome_v3_hg19_capture_targets.bed
2) Sort the BAM file:
[user@@cn3316 ~]$  samtools sort -T /tmp/WISExome_SRR1273288.sorted -o input/WISExome_SRR1273288.sorted.bam input/WISExome_SRR1273288.bam
3) Produce a file suitable for analysis or training from the BAM file:
[user@@cn3316 ~]$ wexome python consam.py  input/WISExome_SRR1273288.sorted.bam SeqCap_EZ_Exome_v3_hg19_capture_targets.bed convert/WISExome_SRR1273288.sorted.hits
[user@@cn3316 ~]$ mkdir leno
[user@@cn3316 ~]$ python lennormalize.py convert SeqCap_EZ_Exome_v3_hg19_capture_targets.bed leno
4) Produce an index for the sorted BAM file (will take several hours to run):
[user@@cn3316 ~]$ samtools index input/WISExome_SRR1273288.sorted.bam
5) Create a reference:
a
[user@@cn3316 ~]$ mkdir refdata
[user@@cn3316 ~]$ ./create_ref.sh 
or, since this step take long to complete, just link the already pre-computed reference data:
a
[user@@cn3316 ~]$ ln -s /fdb/WISExome/refdata
   Combine the results to make a final selection of reference regions for every region on every target chromosome (will take ~ 1 hour):
[user@@cn3316 ~]$ python takeref.py refdata/ refout/WISExome_SRR1273288
1 2
1 3
1 4
1 5
1 6
1 7
...
) Determine unreliable target regions:
[user@@cn3316 ~]$ ln -s convert refsamples
[user@@cn3316 ~]$ ./determine_unreliable_target_regions.sh WISExome_SRR1273288
7) Run tests:
[user@@cn3316 ~]$  mkdir testout 
[user@@cn3316 ~]$ ./run_tests.sh WISExome_SRR1273288 SeqCap_EZ_Exome_v3_hg19_capture_targets.bed
This command will create files:
    testout/*.flameview.pdf,
    testout/*.overview.pdf,
and
    testout/*.pickle.
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$