yogionbioinformatics/joint-genotyping-2021-2022

Joint Genotyping in MIT Fraenkel Lab with ALS Genomics + 1000 Genomes Data

Joint Genotyping 2021-2022

This repository contains all the information to reproduce the Joint Genotyping run from Fall 2021 till Spring 2022.

Chronology:

1. data_engineering/size_estimation/JG_input_data_size_estimation.ipynb
2. data_engineering/data_transfer/transfer.sh
3. data_engineering/delete_duplicates/notebook/choose_representative_sample.ipynb
4. data_engineering/delete_duplicates/output/remove_repeated_samples_data.sh
5. sentieon_joint_genotyping/gvcf_input_file/scripts/create_gvcf_sorted_input_list.sh
6. sentieon_joint_genotyping/shards/notebook/create_shards.ipynb
7. sentieon_joint_genotyping/queue_jobs/queue_jobs.py
   • NOTE: every SLURM script and its output can be found under: sentieon_joint_genotyping/SLURM/
8. data_engineering/data_transfer/transfer_to_MIT_Answer.sh
9. JG_validation/notebooks/validations.ipynb

Representative Overview Figure:

Source

Shard Size VS Cores Grid Search

You can find a Grid Search comparing Shard Size and number of cores for the C3DDB and Engaging clusters under:
HPC_options_benchmarking/