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Title: GitHub - hitbc/AnalysisScripts · GitHub

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Description: Contribute to hitbc/AnalysisScripts development by creating an account on GitHub.

Open Graph Description: Contribute to hitbc/AnalysisScripts development by creating an account on GitHub.

X Description: Contribute to hitbc/AnalysisScripts development by creating an account on GitHub.

Mail addresses
tjiang@hit.edu.cn

Opengraph URL: https://github.com/hitbc/AnalysisScripts

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88 Commits	https://github.com/hitbc/AnalysisScripts/commits/main/
	https://github.com/hitbc/AnalysisScripts/commits/main/
AnnotationStatistics	https://github.com/hitbc/AnalysisScripts/tree/main/AnnotationStatistics
AnnotationStatistics	https://github.com/hitbc/AnalysisScripts/tree/main/AnnotationStatistics
ONT_Pipeline	https://github.com/hitbc/AnalysisScripts/tree/main/ONT_Pipeline
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LICENSE	https://github.com/hitbc/AnalysisScripts/blob/main/LICENSE
LICENSE	https://github.com/hitbc/AnalysisScripts/blob/main/LICENSE
README.md	https://github.com/hitbc/AnalysisScripts/blob/main/README.md
README.md	https://github.com/hitbc/AnalysisScripts/blob/main/README.md
README	https://github.com/hitbc/AnalysisScripts
MIT license	https://github.com/hitbc/AnalysisScripts
	https://github.com/hitbc/AnalysisScripts#analysisscripts
	https://github.com/hitbc/AnalysisScripts#table-of-contents
Alignment	https://github.com/hitbc/AnalysisScripts#Alignment
Variant Calling based on short-reads	https://github.com/hitbc/AnalysisScripts#Variant-Calling-based-on-short-reads
Variant Calling based on long-reads	https://github.com/hitbc/AnalysisScripts#Variant-Calling-based-on-long-reads
Functional Annotation	https://github.com/hitbc/AnalysisScripts#Functional-Annotation
Population genetic analysis	https://github.com/hitbc/AnalysisScripts#Population-genetic-analysis
Statistical Analysis	https://github.com/hitbc/AnalysisScripts#Statistical-Analysis
Reference panel construction and imputation performing	https://github.com/hitbc/AnalysisScripts#Reference-panel-construction-and-imputation-performing
	https://github.com/hitbc/AnalysisScripts#alignment
	https://github.com/hitbc/AnalysisScripts#variant-calling-based-on-short-reads
https://github.com/hall-lab/sv-pipeline	https://github.com/hall-lab/sv-pipeline
	https://github.com/hitbc/AnalysisScripts#variant-calling-based-on-long-reads
	https://github.com/hitbc/AnalysisScripts#functional-annotation
	https://github.com/hitbc/AnalysisScripts#download-dataset
	https://github.com/hitbc/AnalysisScripts#1-annovar-datasets
	https://github.com/hitbc/AnalysisScripts#2-cadd-datasets
https://cadd.gs.washington.edu/download	https://cadd.gs.washington.edu/download
	https://github.com/hitbc/AnalysisScripts#3-ucsc-datasets
	https://github.com/hitbc/AnalysisScripts#4-ensembl-dataset
	https://github.com/hitbc/AnalysisScripts#5-ncbi-dataset
https://ftp.ncbi.nlm.nih.gov/	https://ftp.ncbi.nlm.nih.gov/
	https://github.com/hitbc/AnalysisScripts#liftover
	https://github.com/hitbc/AnalysisScripts#convert-datasets-into-avinput-format
	https://github.com/hitbc/AnalysisScripts#indexing-datasets-for-varnote-annotation
	https://github.com/hitbc/AnalysisScripts#annotation
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	https://github.com/hitbc/AnalysisScripts#4-annotsv-annotation
	https://github.com/hitbc/AnalysisScripts#population-genetic-analysis
here	https://github.com/hitbc/AnalysisScripts/blob/main/population_structure/README.md
	https://github.com/hitbc/AnalysisScripts#statistical-analysis
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	https://github.com/hitbc/AnalysisScripts#reference-panel-construction-and-imputation-performing
	https://github.com/hitbc/AnalysisScripts#population-based-vcf-quality-control-and-filtering
	https://github.com/hitbc/AnalysisScripts#chinese-reference-panel-construction-using-minimac3
	https://github.com/hitbc/AnalysisScripts#construction-of-combined-our-and-1kgp3-reference-panel
	https://github.com/hitbc/AnalysisScripts#genotype-imputation-using-different-reference-panels
	https://github.com/hitbc/AnalysisScripts#pseudo-gwas-dataset-generation-for-impuation
HGDP samples	https://www.internationalgenome.org/data-portal/data-collection/hgdp
	https://github.com/hitbc/AnalysisScripts#imputation-on-the-target-genotype-data
Michigan Imputation Server	https://imputationserver.sph.umich.edu
ChinaMAP	https://github.com/hitbc/AnalysisScripts/blob/main/www.mbiobank.com
WBBC	https://imputationserver.westlake.edu.cn/
	https://github.com/hitbc/AnalysisScripts#calculation-of-estimated-squared-correlation-coefficient-aggregate-r2-for-imputation-accuracy
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