deepvariant
Link to section 'Introduction' of 'deepvariant' Introduction
DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
Home page: https://github.com/google/deepvariant
Link to section 'Versions' of 'deepvariant' Versions
- 1.0.0
- 1.1.0
Link to section 'Commands' of 'deepvariant' Commands
- call_variants
- get-pip.py
- make_examples
- model_eval
- model_train
- postprocess_variants
- run-prereq.sh
- run_deepvariant
- run_deepvariant.py
- settings.sh
- show_examples
- vcf_stats_report
Link to section 'Module' of 'deepvariant' Module
You can load the modules by:
module load biocontainers
module load deepvariant
Link to section 'Example job' of 'deepvariant' Example job
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 deepvariant on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 4
#SBATCH --job-name=deepvariant
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers deepvariant
INPUT_DIR="${PWD}/quickstart-testdata"
DATA_HTTP_DIR="https://storage.googleapis.com/deepvariant/quickstart-testdata"
mkdir -p ${INPUT_DIR}
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/NA12878_S1.chr20.10_10p1mb.bam
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/NA12878_S1.chr20.10_10p1mb.bam.bai
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/test_nist.b37_chr20_100kbp_at_10mb.bed
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/test_nist.b37_chr20_100kbp_at_10mb.vcf.gz.tbi
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/ucsc.hg19.chr20.unittest.fasta
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/ucsc.hg19.chr20.unittest.fasta.fai
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/ucsc.hg19.chr20.unittest.fasta.gz
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/ucsc.hg19.chr20.unittest.fasta.gz.fai
wget -P ${INPUT_DIR} "${DATA_HTTP_DIR}"/ucsc.hg19.chr20.unittest.fasta.gz.gzi
run_deepvariant --model_type=WGS --ref="${INPUT_DIR}"/ucsc.hg19.chr20.unittest.fasta --reads="${INPUT_DIR}"/NA12878_S1.chr20.10_10p1mb.bam --regions "chr20:10,000,000-10,010,000" --output_vcf="output/output.vcf.gz" --output_gvcf="output/output.g.vcf.gz" --intermediate_results_dir "output/intermediate_results_dir" --num_shards=4