On this page... (hide)

  1. 1. Usage
  2. 2. Details

1.  Usage

Population-specific databases from the HapMap project. They provide population-specific variant count and frequences.

% vtools show annotations hapmap -v0
hapmap_ASW_freq-hg18_20100817
hapmap_ASW_freq
hapmap_CEU_freq-hg18_20100817
hapmap_CEU_freq
hapmap_CHB_freq-hg18_20100817
hapmap_CHB_freq
hapmap_CHD_freq-hg18_20100817
hapmap_CHD_freq
hapmap_GIH_freq-hg18_20100817
hapmap_GIH_freq
hapmap_JPT_freq-hg18_20100817
hapmap_JPT_freq
hapmap_LWK_freq-hg18_20100817
hapmap_LWK_freq
hapmap_MEX_freq-hg18_20100817
hapmap_MEX_freq
hapmap_MKK_freq-hg18_20100817
hapmap_MKK_freq
hapmap_TSI_freq-hg18_20100817
hapmap_TSI_freq
hapmap_YRI_freq-hg18_20100817
hapmap_YRI_freq

2.  Details

% vtools show annotation hapmap_CEU_freq
Annotation database hapmap_CEU_freq (version hg18_20100817)
Description:            Allele frequency information of SNP markers of the CEU
  population of phase II and III of the HAPMAP project.
Database type:          variant
Reference genome hg18:  chrom, pos, refallele, otherallele
  rsname                rsname
  chrom                 chromosome
  pos                   1-based position
  strand                strand
  refallele             reference allele
  CEU_refallele_freq    frequency of reference allele
  CEU_refallele_count   Count of reference allele
  otherallele           Other allele
  CEU_otherallele_freq  frequency of other allele
  CEU_otherallele_count Count of other allele
  CEU_totalcount        Total allele count

For example, if you would like to know the allele count and frequencies in hapmap, ESP, and thousand genomes projects, you can

vtools init freq
vtools import mydata.vcf --build hg19  # import data
vtools liftover hg18                   # if your data is in hg19
vtools use dbSNP
vtools use hapmap_ASW_freq
vtools use hapmap_CEU_freq
vtools use hapmap_CHB_freq
vtools use hapmap_CHD_freq
vtools use hapmap_GIH_freq
vtools use hapmap_JPT_freq
vtools use hapmap_LWK_freq
vtools use hapmap_MEX_freq
vtools use hapmap_MKK_freq
vtools use hapmap_TSI_freq
vtools use hapmap_YRI_freq
vtools use ESP
vtools use thousandGenomes

vtools export variant --format csv --header \
    chr pos ref alt rsname \
    ASW_refallele_freq ASW_total_count \
    CEU_refallele_freq CEU_totalcount \
    CHB_refallele_freq CHB_totalcount \
    CHD_refallele_freq CHD_totalcount \
    GIH_refallele_freq GIH_totalcount \
    JPT_refallele_freq JPT_totalcount \
    LWK_refallele_freq LWK_totalcount \
    MEX_refallele_freq MEX_totalcount \
    MKK_refallele_freq MKK_totalcount \
    TSI_refallele_freq TSI_totalcount \
    YRI_refallele_freq YRI_totalcount \
    ESP_all_ref_freq ESP_totalcount \
    ESP_AfricanAmerican_RefFreq ESP_AfricanAmerican_totalcount \
    ESP_EuropeanAmerican_RefFreq EuropeanAmerican_totalcount \
    1kg_REF_FREQ \
--fields  chr pos ref alt dbSNP.name \
    ASW_refallele_freq ASW_totalcount \
    CEU_refallele_freq CEU_totalcount \
    CHB_refallele_freq CHB_totalcount \
    CHD_refallele_freq CHD_totalcount \
    GIH_refallele_freq GIH_totalcount \
    JPT_refallele_freq JPT_totalcount \
    LWK_refallele_freq LWK_totalcount \
    MEX_refallele_freq MEX_totalcount \
    MKK_refallele_freq MKK_totalcount \
    TSI_refallele_freq TSI_totalcount \
    YRI_refallele_freq YRI_totalcount \
    "ESP.AllRefCount * 1.0 / (ESP.AllRefCount + ESP.AllAltCount)" "ESP.AllRefCount + ESP.AllAltCount" \
    "ESP.AfricanAmericanRefCount * 1.0 / (ESP.AfricanAmericanRefCount + ESP.AfricanAmericanAltCount)" \
    "ESP.AfricanAmericanRefCount + ESP.AfricanAmericanAltCount" \
    "ESP.EuropeanAmericanRefCount * 1.0 / (ESP.EuropeanAmericanRefCount + ESP.EuropeanAmericanAltCount)" \
    "ESP.EuropeanAmericanRefCount + ESP.EuropeanAmericanAltCount" \
    thousandGenomes.REF_FREQ_INFO > freq.csv

Or, if you would like to get the frequency across all hapmap populations, you can do

vtools output variant chr pos ref alt dbSNP.name \
    ASW_refallele_freq ASW_totalcount \
    CEU_refallele_freq CEU_totalcount \
    CHB_refallele_freq CHB_totalcount \
    CHD_refallele_freq CHD_totalcount \
    GIH_refallele_freq GIH_totalcount \
    JPT_refallele_freq JPT_totalcount \
    LWK_refallele_freq LWK_totalcount \
    MEX_refallele_freq MEX_totalcount \
    MKK_refallele_freq MKK_totalcount \
    TSI_refallele_freq TSI_totalcount \
    YRI_refallele_freq YRI_totalcount \
"(IFNULL(ASW_refallele_count, 0.) + \
    IFNULL(CEU_refallele_count, 0.) + \
    IFNULL(CHB_refallele_count, 0.) + \
    IFNULL(CHD_refallele_count, 0.) + \
    IFNULL(GIH_refallele_count, 0.) + \
    IFNULL(JPT_refallele_count, 0.) + \
    IFNULL(LWK_refallele_count, 0.) + \
    IFNULL(MEX_refallele_count, 0.) + \
    IFNULL(MKK_refallele_count, 0.) + \
    IFNULL(TSI_refallele_count, 0.) + \
    IFNULL(YRI_refallele_count, 0.)) * 1.0 / \
    (IFNULL(ASW_totalcount, 0) + \
    IFNULL(CEU_totalcount, 0) + \
    IFNULL(CHB_totalcount, 0) + \
    IFNULL(CHD_totalcount, 0) + \
    IFNULL(GIH_totalcount, 0) + \
    IFNULL(JPT_totalcount, 0) + \
    IFNULL(LWK_totalcount, 0) + \
    IFNULL(MEX_totalcount, 0) + \
    IFNULL(MKK_totalcount, 0) + \
    IFNULL(TSI_totalcount, 0) + \
    IFNULL(YRI_totalcount, 0))"  -l 10

Here IFNULL is used to convert missing values to 0, and the result will be NULL if total count is 0 (which leads to 0./0).