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
- 1.02
- clairvoyante.py
You can load the modules by:
module load biocontainers module load clairvoyante
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