This repository contains all the information to reproduce the Joint Genotyping run from Fall 2021 till Spring 2022.
data_engineering/size_estimation/JG_input_data_size_estimation.ipynb
data_engineering/data_transfer/transfer.sh
data_engineering/delete_duplicates/notebook/choose_representative_sample.ipynb
data_engineering/delete_duplicates/output/remove_repeated_samples_data.sh
sentieon_joint_genotyping/gvcf_input_file/scripts/create_gvcf_sorted_input_list.sh
sentieon_joint_genotyping/shards/notebook/create_shards.ipynb
sentieon_joint_genotyping/queue_jobs/queue_jobs.py
- NOTE: every SLURM script and its output can be found under:
sentieon_joint_genotyping/SLURM/
- NOTE: every SLURM script and its output can be found under:
data_engineering/data_transfer/transfer_to_MIT_Answer.sh
JG_validation/notebooks/validations.ipynb
You can find a Grid Search
comparing Shard Size
and number of cores
for the C3DDB
and Engaging
clusters under:
HPC_options_benchmarking/