1.chr22.vcf.gz
来自：ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/1kGP_high_coverage_Illumina.chr22.filtered.SNV_INDEL_SV_phased_panel.vcf.gz
实际样本数为3690,样本信息见sample_summary_3690.txt

2.GSA-24v3_chr_pos.list
来自：https://support.illumina.com/content/dam/illumina-support/documents/downloads/productfiles/global-screening-array-24/v3-0/GSA-24v3-0-A2-manifest-file-csv.zip
仅提取染色体和位置信息

3.samples_population_3202.txt
来自：https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt
AMR => 490 => Ad Mixed American
AFR => 893 => African
EUR => 633 => European
EAS => 585 => East Asian
SAS => 601 => South Asian
其中 EAS+SAS构建PanelA[去除20个测试样本后共1166个样本,PanelA_sample.list]， 
     AMR+AFR+EUR构建PanelB[去除30个测试样本后共1986个样本,PanelB_sample.list]，
     A+B为PanelO[共3152样本,PanelO_sample.list]

4.sample_summary_3690.tx
来自：https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/20140502_sample_summary_info/20140502_complete_sample_summary.txt

5.test_sample
50个测试样本及imputed输出,以样本SAS_NA20872为例：
  SAS_NA20872_chip.meta_chr22.imputed.metaDose.vcf.gz           # MetaMinimac2 输出结果[chip_subset]
  SAS_NA20872_chip.PanelA_chr22.imputed.dose.vcf.gz		        # Minimac4 PanelA 输出结果[chip_subset]
  SAS_NA20872_chip.PanelA_chr22.imputed.empiricalDose.vcf.gz    
  SAS_NA20872_chip.PanelA_chr22.imputed.info
  SAS_NA20872_chip.PanelB_chr22.imputed.dose.vcf.gz             # Minimac4 PanelB 输出结果[chip_subset]
  SAS_NA20872_chip.PanelB_chr22.imputed.empiricalDose.vcf.gz
  SAS_NA20872_chip.PanelB_chr22.imputed.info
  SAS_NA20872_chip.PanelO_chr22.imputed.dose.vcf.gz             # Minimac4 PanelO 输出结果[chip_subset]
  SAS_NA20872_chip.PanelO_chr22.imputed.empiricalDose.vcf.gz
  SAS_NA20872_chip.PanelO_chr22.imputed.info
  SAS_NA20872_chip.vcf						# GSA芯片22号染色体共计9183个位点，vcf中存在并保留的位点数为8516个位点
  SAS_NA20872.meta_chr22.imputed.metaDose.vcf.gz                
  SAS_NA20872.PanelA_chr22.imputed.dose.vcf.gz
  SAS_NA20872.PanelA_chr22.imputed.empiricalDose.vcf.gz
  SAS_NA20872.PanelA_chr22.imputed.info
  SAS_NA20872.PanelB_chr22.imputed.dose.vcf.gz
  SAS_NA20872.PanelB_chr22.imputed.empiricalDose.vcf.gz
  SAS_NA20872.PanelB_chr22.imputed.info
  SAS_NA20872.PanelO_chr22.imputed.dose.vcf.gz
  SAS_NA20872.PanelO_chr22.imputed.empiricalDose.vcf.gz
  SAS_NA20872.PanelO_chr22.imputed.info
  SAS_NA20872.vcf                                               # 样本原始vcf文件，共计1066557个位点
  SAS_NA20872_chip_imputed_compare.txt                          # 原始样本和两种填充方法，按位点比较一致性输出文件

6.Imputed_compare.summary
最终比较结果汇总，分基因型统计，source字段表示原始vcf中的位点数, mac4字段表示Minimac4充填与原始文件一致位点数的比率，meta为MetaMinimac2充填一致位点比率。
最后两列为所有基因型一致位点两种方法的比率。

7.Imputed_compare.log
两种方法比较输出日志

8.PanelO_chr22_group_alt_af.txt
对PanelO中的3152样本，统计每个位点在不同群体中的AF

9.Imputed_r2_test.summary
pearson correlation 测试结果，按样本按群体按AF-bin输出结果

10.Imputed_r2_test.log
pearson correlation 测试日志，包括选取的位点，及位点对应基因型的测试数据集

11.Imputed_r2_test_page.json
pearson correlation 测试Avg r2结果，AF数据log10处理, 用于html网页加载展示

12.Imputed_r2_test_page.html
Avg r2可视化作图