Sniffles2¶

Description¶

A fast structural variant caller for long-read sequencing, Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.

Environment Modules¶

Run module spider sniffles2 to find out what environment modules are available for this application.

Environment Variables¶

HPC_SNIFFLES2_DIR - installation directory
HPC_SNIFFLES2_BIN - executable directory

Job Script Examples¶

Example job script used for testing application installation:

#!/bin/bash
#SBATCH --job-name=sniffles2_2.0.6_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2gb
#SBATCH --time=24:00:00
#SBATCH --output=sniffles2_2.0.6_test.log

echo "Setting up test environment..."
TEST_PWD=/data/apps/tests/sniffles2/2.0.6
TEST_DATADIR=${TEST_PWD}/example_data
TEST_WORKDIR=${TEST_PWD}/test_output

cd ${TEST_PWD}
module load sniffles2/2.0.6

# Remove any previous test results and re-create a working directory
if [ -d ${TEST_WORKDIR} ]; then rm -rf ${TEST_WORKDIR}/; fi
mkdir ${TEST_WORKDIR}

echo "Starting test run at $(date) on $(hostname)..."

###################################
sniffles \
    --input ${TEST_DATADIR}/mapt.NA12156.altex.bam \
    --vcf ${TEST_WORKDIR}/test1.vcf.gz \
    --snf ${TEST_WORKDIR}/test1.snf \
    --threads ${SLURM_CPUS_ON_NODE:-4}
###################################

# There should be some files in the work directory
echo "There should be some results listed below:"
find ${TEST_WORKDIR} -type f ! -empty -ls

echo "Test complete at $(date)."

Citation¶

If you publish research that uses Sniffles2 you have to cite it as follows:

Sedlazeck, F.J., Rescheneder, P., Smolka, M. et al. Accurate detection of complex structural variations using single-molecule sequencing. Nat Methods 15, 461–468 (2018). https://doi.org/10.1038/s41592-018-0001-7

Comprehensive Structural Variant Detection: From Mosaic to Population-Level. Moritz Smolka, Luis F. Paulin, Christopher M. Grochowski, Medhat Mahmoud, Sairam Behera, Mira Gandhi, Karl Hong, Davut Pehlivan, Sonja W. Scholz, Claudia M.B. Carvalho, Christos Proukakis, Fritz J Sedlazeck. https://doi.org/10.1101/2022.04.04.487055

Categories¶

biology