HapMap

http://zzz.bwh.harvard.edu/plink/res.shtml#hapmap

1000G

https://www.cog-genomics.org/plink/1.9/resources

Reference

• A guide to genome-wide association analysis and post-analytic interrogation, 2015
• PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses, 2007
• Genotyping and quality control of UK Biobank, a large-scale, extensively phenotyped prospective resource, 2015
• A Statistical Approach to Genetic Epidemiology, 2010
• Analysis of Genetic Association Studies, 2012

Helpful

• Resequencing
• NGS 분석의 기초 개념
• Introduction to NGS data analysis
• Informatics on High-throughput Sequencing Data
• Introduction to Variant Calling
• Assembly
• 유전체 크기 예측
• Repeat Masker

About reference genome

• NCBI 1000genomes : GRCh38
• BWA github
• Which human reference genome to use?
• How to Download hg38/GRCh38 FASTA Human Reference Genome
• ebi.ac.uk masked fa
• Reference fa files

Gene list

• ADNI 63
• ADNI : APOE ABCA7 DSG2 FERMT2 CLU
• ADNI : EPHA1 PICALM PTK2B ZCWPW1 SORL1
• PPMI, NCBI : LRRK2 PARK7 PINK1 PARK2 SNCA
• MDD : HTR2A SLC6A2 NR3C1 BDNF TPH2 PCLO
• MDD : ATP6V1B2 GRM7 SP4
• 1000K : TCF7L2 ABCC8 CAPN10 GLUT2 GCGR
• TB : NRAMP1 SLC11A1 HLA-DRB1 VDR IFNG
• Avellino : EFEMP2 LTBP2 ZNF469 LOX LOXL1
• 1000G : PDX1 RFX6 HNF1B MEIS1

Trio data

• Reference

  • Daughter, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/10Xgenomics_ChromiumGenome_LongRanger2.1_09302016/NA12878_GRCh38/
  • Daughter, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv3.3.2/GRCh38/
  • Father, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/technical/10Xgenomics_ChromiumGenome_LongRanger2.1_09302016/NA12891_GRCh38/
  • Mother, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/technical/10Xgenomics_ChromiumGenome_LongRanger2.1_09302016/NA12892_GRCh38/

• Chinese

  • Son, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG005_NA24631_son/NISTv3.3.2/GRCh38/
  • Father, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG006_NA24694_father/NISTv3.3.2/GRCh38/
  • Mother, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/ChineseTrio/HG007_NA24695_mother/NISTv3.3.2/GRCh38/

• Ashkenazim

  • Son, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv3.3.2/GRCh38/
  • Son, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.1/GRCh38/
  • Father, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG003_NA24149_father/NISTv3.3.2/GRCh38/
  • Mother, ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/AshkenazimTrio/HG004_NA24143_mother/NISTv3.3.2/GRCh38/