snakemake-gatk4-non-model

germline variant calling

Working with non-model organism means you don't have known SNPs and prepared interval list in GATK bundle. Alternatively I did:

• Optional Base Quality Score Calibration(BQSR) (working...)
• Apply hard filters to call sets.
• Split genome into scaffolds as intervals.

How to run:

0. conda env create -f environment.yaml and install bamcov ...
1. prepare metadata.tsv.
2. modify config.yaml if needed.
3. snakemake

To run on JCU HPC with PBSpro:

snakemake -p --cluster-config jcu_hpc.json --cluster "qsub -j oe -l walltime={cluster.time} -l select=1:ncpus={cluster.ncpus}:mem={cluster.mem}" --jobs 100 --latency-wait 5

Clean everything:

snakemake clean

Reference:

https://snakemake.readthedocs.io/en/stable/ https://github.com/gatk-workflows/gatk4-germline-snps-indels https://github.com/snakemake-workflows/dna-seq-gatk-variant-calling https://zhuanlan.zhihu.com/p/33891718 https://software.broadinstitute.org/gatk/documentation/article?id=11097 https://gatkforums.broadinstitute.org/gatk/discussion/12443/genomicsdbimport-run-slowly-with-multiple-samples