WISARD[wɪzərd]
Workbench for Integrated Superfast Association study with Related Data
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Case tutorial

  1. Study design
  2. Data management
  3. Summary statistics
  4. Association analysis
  5. Miscellaneous
 

Fixation Index (FST)

The fixation index (FST) is a measure of population differentiation due to genetic structure. It is frequently estimated from genetic polymorphism data, such as single-nucleotide polymorphisms (SNP) or microsatellites. Developed as a special case of Wright's F-statistics, it is one of the most commonly used statistics in population genetics. (From Wikipedia).

Fixation index FST can be calculated with group information and genomic information-based approaches. WISARD can calculate FST by using --fst option, with below options.

  • --sampvar to assign group information for samples.
  • --fst to indicate which column is stands for group information for samples.
  • Optionally --set to get FST by grouping multiple variants together.

Consider the example code with samples:

Example 1 : Example sample variable file
FID	IID	FST_GROUP	AGE
FAM1	SAMP1	KOREAN	37
FAM2	SAMP2	KOREAN	27
FAM3	SAMP3	KOREAN	32
FAM4	SAMP4	KOREAN	55
FAM5	SAMP5	KOREAN	17
FAM6	SAMP6	KOREAN	39
FAM7	SAMP7	JAPANESE	23
FAM8	SAMP8	JAPANESE	28
FAM9	SAMP9	JAPANESE	61
FAM10	SAMP10	JAPANESE	44
Computing variant-wise FST C:\Users\WISARD> wisard --bed test_miss0.bed --fst region --sampvar test_miss0_phen.txt --out res_fst

Compute group-wise FST

In default, FST is computed variant-wise, but it is possible to compute FST from multiple variants. In order to use this, a proper gene-variant mapping is required. For detail, please refer Set file format section on this page.

Computing group-wise FST C:\Users\WISARD> wisard --bed test_miss0.bed --fst region --sampvar test_miss0_phen.txt --set test_gene.txt --out res_fst_group


Output file [top]

Running the above command produces the output file, fst.res. The meaning of each column in output file is:

fst.res is... A result of FST estimation (TSV)
Column Format Modifier Description
CHR real NONE GWAS-level estimated power
VARIANT real NONE GWAS-level estimated power
POS real NONE GWAS-level estimated power
ALT real NONE GWAS-level estimated power
ANNOT real NONE GWAS-level estimated power
Fst real NONE FST value
GENE string --set Group name of Fst computed
NVARIANT integer --set Number of variants in the group


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Last modified : 2017-09-13 16:35:13

Prof. Won's labratory and Bioinformatics and Biostatistics (BIBS) labratory, Seoul National University.

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