Introduction ~~~~~~~~ Clairvoyante is a deep neural network based variant caller.
For more information, please check:
Docker hub: https://hub.docker.com/r/lifebitai/clairvoyante
Home page: https://github.com/aquaskyline/Clairvoyante
Docker hub: https://hub.docker.com/r/lifebitai/clairvoyante
Home page: https://github.com/aquaskyline/Clairvoyante
- 1.02
Commands ~~~~~~~ - clairvoyante.py
You can load the modules by:
module load biocontainers
module load clairvoyante
Example job ~~~~~ .. warning:: Using #!/bin/sh -l
as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash
instead.
To run clairvoyante on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=clairvoyante
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers clairvoyante
cd training
clairvoyante.py callVarBam \
--chkpnt_fn ../trainedModels/fullv3-illumina-novoalign-hg001+hg002-hg38/learningRate1e-3.epoch500 \
--bam_fn ../testingData/chr21/chr21.bam \
--ref_fn ../testingData/chr21/chr21.fa \
--bed_fn ../testingData/chr21/chr21.bed \
--call_fn chr21_calls.vcf \
--ctgName chr21