The svanna is an efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing.

References:

• Danis, D., Jacobsen, J.O.B., Balachandran, P. et al. SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing.Genome Med 14, 44 (2022) Journal

• svanna Github:Github
• svanna doc:Github

• Module Name: svanna (see the modules page for more information)
• The svanna ((available on biowulf) command lines could be run as:

  	java -jar $SVANNA_PATH/svanna-cli-1.0.3.jar prioritize -d $SVANNA_DB/2304 --help
  	

• svanna database in $SVANNA_DB
• svanna testing vcf in $SVANNA_TEST_DATA

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf]8$ sinteractive --mem=8g
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 svanna
[user@cn3144 ~]$ mkdir /data/$USER/svanna_test/
[user@cn3144 ~]$ cd /data/$USER/svanna_test/
[user@cn3144 ~]$ java -jar $SVANNA_PATH/svanna-cli-1.0.3.jar prioritize -d $SVANNA_DB/2304 --help
Prioritize the variants.
Usage: svanna-cli.jar prioritize [-hVv] [--no-breakends] [--uncompressed-output] -d=path/to/datadir
                                 [--frequency-threshold=] [--ic-mica-mode={DATABASE,IN_MEMORY}]
                                 [--min-read-support=] [--n-threads=2] [--out-dir=]
                                 [--output-format=html] [--overlap-threshold=] [-p=]
                                 [--prefix=] [--promoter-fitness-gain=]
                                 [--promoter-length=] [--report-top-variants=100]
                                 [--term-similarity-measure={RESNIK_SYMMETRIC, RESNIK_ASYMETRIC}] [--vcf=]
                                 [-t=]...
  -v                         Specify multiple -v options to increase verbosity.
                             For example, `-v -v -v` or `-vvv`
  -d, --data-directory=path/to/datadir
                             Path to SvAnna data directory.
  -h, --help                 Show this help message and exit.
  -V, --version              Print version information and exit.
SvAnna configuration:
      --term-similarity-measure={RESNIK_SYMMETRIC, RESNIK_ASYMETRIC}
                             Phenotype term similarity measure (default: RESNIK_SYMMETRIC).
      --ic-mica-mode={DATABASE,IN_MEMORY}
                             The mode for getting information content of the most informative common ancestors for
                               terms t1, and t2 (default: DATABASE).
      --promoter-length=
                             Number of bases prepended to a transcript and evaluated as a promoter region (default:
                               2000).
      --promoter-fitness-gain=
                             Set to 0. to score the promoter variants as strictly as coding variants, or to 1. to skip
                               them altogether (default: 0.6).
Analysis input:
  -p, --phenopacket=
                             Path to v1 or v2 phenopacket in JSON, YAML or Protobuf format.
  -t, --phenotype-term=
                             HPO term ID(s). Can be provided multiple times.
      --vcf=            Path to the input VCF file.
Run options:
      --frequency-threshold=
                             Frequency threshold as a percentage [0-100] (default: 1.0).
      --overlap-threshold=
                             Percentage threshold for determining variant's region is similar enough to database entry
                               (default: 80.0).
      --min-read-support=
                             Minimum number of ALT reads to prioritize (default: 3).
      --n-threads=2          Process variants using n threads (default: 2).
Output options:
      --no-breakends         Do not include breakend variants into HTML report (default: false).
      --output-format=html   Comma separated list of output formats to use for writing the results (default: html).
      --out-dir=     Path to folder where to write the output files (default: current working directory).
      --prefix=   Prefix for output files (default: based on the input VCF name).
      --report-top-variants=100
                             Report top n variants (default: 100).
      --uncompressed-output  Write tabular and VCF output formats with no compression (default: false).
See the full documentation at `https://svanna.readthedocs.io/en/master`

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

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

#!/bin/bash
set -e
module load svanna
cp $SVANNA_TEST_DATA/*.vcf .
java -jar $SVANNA_PATH/svanna-cli-1.0.3.jar prioritize -d $SVANNA_DB/2304 --vcf example.vcf  --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147

Submit this job using the Slurm sbatch command.

sbatch --mem=8g svanna.sh

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

java -jar $SVANNA_PATH/svanna-cli-1.0.3.jar prioritize -d $SVANNA_DB/2304 --vcf example1.vcf --out-dir results --prefix example1  --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147
java -jar $SVANNA_PATH/svanna-cli-1.0.3.jar prioritize -d $SVANNA_DB/2304 --vcf example2.vcf --out-dir results --prefix example2  --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147

Submit this job using the swarm command.

swarm -f svanna.swarm [-t #] [-g #] --module svanna