SVTK: Utilities for consolidating, filtering, resolving, and annotating structural variants. It was wrote by Talkowski lab.

References:

• Ryan L. collins et.al. A structural variation reference for medical and population genetics. Nature 2020 PubMed |  Journal

• Source code repository: on GitHub

• Module Name: svtk (see the modules page for more information)
• Example data in $SVTK_TEST_DATA

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

[user@biowulf]$ sinteractive --mem=4g
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 ~]$ module load svtk
[+] Loading svtk  0.1

[user@cn3144 ~]$ svtk
usage: svtk [-h]  [options]
[ Preprocessing ]
    standardize    Convert SV calls to a standardized format.
    rdtest2vcf     Convert an RdTest-formatted bed to a standardized VCF.
    vcf2bed        Convert a standardized VCF to an RdTest-formatted bed.

[ Algorithm integration ]
    vcfcluster     Cluster SV calls from a list of VCFs. (Generally PE/SR.)
    bedcluster     Cluster SV calls from a BED. (Generally depth.)

[ Statistics ]
    count-svtypes  Count instances of each svtype in each sample in a VCF

[ Read-depth analysis ]
    bincov         Calculate normalized genome-wide depth of coverage.
    rdtest*        Calculate comparative coverage statistics at CNV sites.

[ PE/SR analysis ]
    collect-pesr   Count clipped reads and extract discordant pairs genomewide.
    sr-test        Calculate enrichment of clipped reads at SV breakpoints.
    pe-test        Calculate enrichment of discordant pairs at SV breakpoints.

[ Variant analysis ]
    resolve        Resolve complex variants from VCF of breakpoints.
    annotate       Annotate genic effects and ovelrap with noncoding elements.




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

Create a batch input file (e.g. svtk.sh), which uses the input file 'svtk.in'. For example:

#! /bin/bash

module load svtk || exit 1
svtk  [options]

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=10g  --gres=lscratch:20 svtk.sh

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

svtk  [options]
svtk  [options]

Submit this job using the swarm command.

swarm -f svtk.swarm -g 10 --module svtk --gres=lscratch:10