SMC++¶

Description¶

smcpp website

SMC++ is a program for estimating the size history of populations from whole genome sequence data.

Environment Modules¶

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

Environment Variables¶

HPC_SMCPP_DIR - installation directory
HPC_SMCPP_BIN - executable directory

Job Script Examples¶

Example job script used for testing application installation:

#!/bin/bash
#SBATCH --job-name=smcpp_test
#SBATCH --mail-type=NONE
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=1gb
#SBATCH --time=24:00:00
#SBATCH --output=smcpp_test.log

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

cd ${TEST_PWD}
module load smcpp

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

cp ${TEST_DATADIR}/* ${TEST_WORKDIR}

cd ${TEST_WORKDIR}

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

###################################
echo "   Converting VCF to SMC using vcf2smc subcommand..."
smc++ \
    vcf2smc \
    ${TEST_DATADIR}/example.vcf.gz \
    ${TEST_WORKDIR}/test.smc \
    1 \
    CEU:msp_0,msp_1

echo "   Estimating using estimate subcommand..."
smc++ \
    estimate \
    1e-8 \
    ${TEST_WORKDIR}/test.smc \
    -o ${TEST_WORKDIR}/output \
###################################

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

echo "Test complete at $(date)."

Citation¶

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

J. Terhorst, J. A. Kamm, and Y. S. Song. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nature Genetics, 49(2):303–309, 2017. https://doi.org/10.1038/ng.3748

Categories¶

biology, genomics, sequencing