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Latest commit

aleksandr-medvedev-msc

Fixed ibis_king workflow

Jul 28, 2023

a997db9 · Jul 28, 2023

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Name		Name	Last commit message	Last commit date
parent directory ..
test_data		test_data	Working plotting of ibd segments detection accuracy	Oct 22, 2020
utils		utils	[GRAPE-124] Fixed reading from bcftools	Feb 3, 2023
client_background_test.py		client_background_test.py	Temp fixes in pre_imputation_check	Apr 13, 2023
ersa_king.py		ersa_king.py	Fixed vcf_to_ped conversion using scikit-allel and zarr	Dec 1, 2020
estimate_ersa_params.py		estimate_ersa_params.py	Small commit	Oct 21, 2020
estimate_rapid_params.py		estimate_rapid_params.py	Simulation with rapid flow	Feb 10, 2023
evaluate.py		evaluate.py	Fixed polars, pydor and other dependencies, removed conda envs	Jul 28, 2023
filter_aadr.py		filter_aadr.py	script to select only modern samples from aadr dataset	Apr 21, 2023
filter_reference_panel.py		filter_reference_panel.py	Built a new reference imputation panel, fixed some bugs in merge_king…	Mar 12, 2021
filter_reference_panel.sh		filter_reference_panel.sh	Built a new reference imputation panel, fixed some bugs in merge_king…	Mar 12, 2021
ibis_mapping.py		ibis_mapping.py	Create ibis_mapping.py	Jan 14, 2022
interpolate.py		interpolate.py	Fixed polars, pydor and other dependencies, removed conda envs	Jul 28, 2023
merge_ibd.py		merge_ibd.py	Fixes of main worklflow	Nov 10, 2020
merge_king_ersa.py		merge_king_ersa.py	Fixed ibis_king workflow	Jul 28, 2023
plink_filter.py		plink_filter.py	minor changes in error detection	May 16, 2022
postprocess.py		postprocess.py	Remove hapmap [BAR-23]	Mar 9, 2022
postprocess_ersa.py		postprocess_ersa.py	Fixed polars, pydor and other dependencies, removed conda envs	Jul 28, 2023
pre_imputation_check.py		pre_imputation_check.py	Added back annotate id bcftools rule to standard preprocessing	Apr 14, 2023
remove_imputation.py		remove_imputation.py	Added new preprocessing, it can do optional lifting, phasing and impu…	Mar 23, 2021
remove_relatives.py		remove_relatives.py	remove_relatives workflow now outputs unrelated samples	Apr 10, 2023
select_bad_samples.py		select_bad_samples.py	Fixed polars, pydor and other dependencies, removed conda envs	Jul 28, 2023
shuffle_phase.py		shuffle_phase.py	Working confusion matrix plot	Apr 3, 2021
simulate_dummy_samples.py		simulate_dummy_samples.py	Fixed polars, pydor and other dependencies, removed conda envs	Jul 28, 2023
split_chip.py		split_chip.py	Configurable simbig background augmentation	Jul 18, 2023
split_map.py		split_map.py	almost	Dec 15, 2020
transform_ibis_segments.py		transform_ibis_segments.py	grape launches several ibis processes in parallel for different chrom…	Jun 23, 2023
transform_rapid_segments.py		transform_rapid_segments.py	Small fixes of preprocessing and postprocessing	Feb 21, 2023
vcf_to_ped.py		vcf_to_ped.py	Updated preprocessing and phasing parameters	Mar 31, 2021
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