NAP-MED_lab_script

here list all the scripts I usually used in the lab (PRS calculation, QC, ....)

Name		Name	Last commit message	Last commit date
Latest commit History 12 Commits
.ipynb_checkpoints		.ipynb_checkpoints
Exomedepth		Exomedepth
Genotype_QC_Package_NIH_TOPMed		Genotype_QC_Package_NIH_TOPMed
MIPs		MIPs
PRS		PRS
pathway_PRS		pathway_PRS
segregation_analysis_bygene		segregation_analysis_bygene
.gitignore		.gitignore
EA_PD_MRAPSS.RData		EA_PD_MRAPSS.RData
Nanuq_remove_dup_ID.py		Nanuq_remove_dup_ID.py
README.md		README.md
STEP1_pre_imputation_step.sh		STEP1_pre_imputation_step.sh
STEP1_pre_imputation_step_no_ancestry_no_relatedness.sh		STEP1_pre_imputation_step_no_ancestry_no_relatedness.sh
add_rsid_hg38_vcf.sh		add_rsid_hg38_vcf.sh
add_rsid_to_imputed_plink.sh		add_rsid_to_imputed_plink.sh
add_rsid_to_imputed_plink_hg38.sh		add_rsid_to_imputed_plink_hg38.sh
add_rsid_to_imputed_plink_no_pos.sh		add_rsid_to_imputed_plink_no_pos.sh
add_zscore_column_from_plink_gwas.sh		add_zscore_column_from_plink_gwas.sh
ancestry.sh		ancestry.sh
annovar.vcf.sh		annovar.vcf.sh
change_X_to_23.py		change_X_to_23.py
change_name.sh		change_name.sh
chr_name_conv.txt		chr_name_conv.txt
convert_back_position_to_rsid.r		convert_back_position_to_rsid.r
convert_rsid_to_GRCh38_position.r		convert_rsid_to_GRCh38_position.r
convert_z.py		convert_z.py
f.sh		f.sh
find_genes_ensembl.r		find_genes_ensembl.r
get_columns_from_PRS_all_score.py		get_columns_from_PRS_all_score.py
get_database_info.R		get_database_info.R
get_database_info_short.R		get_database_info_short.R
get_non_actg_snps_no_duplicate_snps.py		get_non_actg_snps_no_duplicate_snps.py
liftover.sh		liftover.sh
make_plink-files_from_imputed_vcf.sh		make_plink-files_from_imputed_vcf.sh
make_plink_from_topmed_vcf_new.sh		make_plink_from_topmed_vcf_new.sh
map_genes_GRCh37.py		map_genes_GRCh37.py
map_genes_GRCh38.py		map_genes_GRCh38.py
merge_afterlift.py		merge_afterlift.py
prep_omnix_from-nanuq_nodup.sh		prep_omnix_from-nanuq_nodup.sh
relatedness.sh		relatedness.sh
remove_high_F_coef.r		remove_high_F_coef.r
run.sh		run.sh
sex_check.r		sex_check.r
step0_make_bim_files.out		step0_make_bim_files.out
step0_make_bim_files1.out		step0_make_bim_files1.out
step0_make_bim_files_B.out		step0_make_bim_files_B.out
write_prelift.py		write_prelift.py

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