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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:

• Roy Straver, Marjan M. Weiss, Quinten Waisfisz, Erik A. Sistermans, Marcel J. T. Reinders
  WISExome: a within-sample comparison approach to detect copy number variations in whole exome sequencing data.
  European Journal of Human Genetics 2017, 25: 1354-1363, doi: https://doi.org/10.1038/s41431-017-0005-2.

• WISExome Github page

• Module Name: WISExome (see the modules page for more information)
• Implemented as a Singularity container
• Unusual environment variables set
  • WEXOME_HOME  WISExome installation directory
  • WEXOME_BIN       WISExome executable directory
  • WEXOME_DATA    WISExome test data directory
• Example file in $WEXOME_TEST

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 ~]$