Biowulf High Performance Computing at the NIH
AnnotSV on Biowulf

AnnotSV is a program designed for annotating Structural Variations (SV). This tool compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positives.

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=10g
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 ~]$ cp -r /usr/local/apps/annotsv/Example/* .

[user@cn3144 ~]$ cd Example

[user@cn3144 ~]$ module load annotsv
[+] Loading annotsv  1.1.1  on cn3144 
[+] Loading tcl_tk 8.6.8 

[user@cn3144 ~]$ AnnotSV -SVinputFile test.bed -SVinputInfo 1 -outputFile ./test.annotated.tsv
AnnotSV 1.1.1

Copyright (C) 2017-2018 GEOFFROY Veronique

Please feel free to contact me for any suggestions or bug reports
email: veronique.geoffroy@inserm.fr

Tcl/Tk version: 8.6

Application name used (defined with the "ANNOTSV" environment variable):
/usr/local/apps/annotsv/1.1.1


...downloading the configuration data (September 13 2018 - 12:59)
  ...configuration data by default
  ...configuration data from /usr/local/apps/annotsv/1.1.1/configfile
  ...configuration data given in arguments
  ...checking configuration data and files
[...]
...Output columns annotation:
  SV chrom; SV start; SV end; ; ; AnnotSV type; Gene name; NM; CDS length; tx length; location; intersectStart; intersectEnd; promoters; DGV_GAIN_IDs; DGV_GAIN_n_samples_with_SV; DGV_GAIN_n_samples_tested; DGV_GAIN_Frequency; DGV_LOSS_IDs; DGV_LOSS_n_samples_with_SV; DGV_LOSS_n_samples_tested; DGV_LOSS_Frequency; DDD_SV; DDD_DUP_n_samples_with_SV; DDD_DUP_Frequency; DDD_DEL_n_samples_with_SV; DDD_DEL_Frequency; 1000g_event; 1000g_AF; 1000g_max_AF; DDD_status; DDD_mode; DDD_consequence; DDD_disease; DDD_pmids; synZ; misZ; pLI; HI_percent; Mim Number; Phenotypes; Inheritance; GCcontent_left; GCcontent_right; Repeats_coord_left; Repeats_type_left; Repeats_coord_right; Repeats_type_right; TADcoordinates; ENCODEexperiments


...AnnotSV is done with the analysis (September 13 2018 - 12:59)


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

Batch job
Most jobs should be run as batch jobs.

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

#!/bin/bash
module load annotsv
AnnotSV -SVinputFile test.bed -SVinputInfo 1 -outputFile ./test.annotated.tsv

Submit this job using the Slurm sbatch command.

sbatch annotsv.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

AnnotSV -SVinputFile test1.bed -SVinputInfo 1 -outputFile ./test1.annotated.tsv
AnnotSV -SVinputFile test2.bed -SVinputInfo 1 -outputFile ./test2.annotated.tsv
AnnotSV -SVinputFile test3.bed -SVinputInfo 1 -outputFile ./test3.annotated.tsv

Submit this job using the swarm command.

swarm -f annotsv.swarm -g 10 --module annotsv
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module annotsv Loads the annotsv module for each subjob in the swarm