CCEGA HAPMAP Simulator - Output formats for Trios

This page describes the output formats for trios
  In all instances, 0 represents the major allele, 1 represents the minor allele.
Genotypes are coded as the number of minor alleles, so genotypes can assume the values 0,1, or 2.

A trio is formed as a maternal (m), paternal (p), and child (c) combination of simulated transmitted case chromosomes (case_chr)
and non-transmitted control chromosomes (ctrl_chr). The case and control chromosomes are simulated exactly as in a case-control study.
Thus we implicitly assume ascertainment is based on the affected child, irrespective of the parental disease status.

diagram

   

The haplotype output format: 

      

column 1: chromosome number 
column 2: SNP ID
column 3: physical location of the SNP
column 4: minor allele frequency of the SNP in HapMap CEU trios
column 5 and 6: maternal pair of 1st trio
column 6 and 7: child pair of 1st trio
column 7 and 8: paternal pair of 1st trio
column 9 and 10: maternal pair of 2nd trio
column 10 and 11: child pair of 2nd trio
column 11 and 12: paternal pair of 2nd trio
etc.




An example with 5 SNPs, 10 trios:      
      
10	rs1247696	29826038	0.01666667	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
10	rs6481613	29831217	0.41666667	1	0	1	0	0	1	1	0	0	0	1	0	0	0	1	1	0	0	0	1	0	0	0	1	1	1	1	1	0	1	0	1	1	1	0	1	0	0	1	0	
10	rs2182402	29835030	0.41666667	1	0	1	0	0	1	1	0	0	0	1	0	0	0	1	1	0	0	0	1	0	0	0	1	1	1	1	1	0	1	0	1	1	1	0	1	0	0	1	0	
10	rs4747667	29840416	0.36666667	1	0	1	0	0	1	1	0	0	0	1	0	0	0	0	1	0	0	0	1	0	0	0	1	1	1	1	1	0	1	0	1	1	0	0	1	0	0	1	0	
10	rs3740003	29844044	0.25000000	1	0	1	0	0	1	0	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	1	1	0	1	1	0	1	0	1	1	0	0	1	0	0	1	0	

      


      The genotype output format:
      

column 1: the chromosome number
column 2: the SNP ID
column 3: Physical location of the SNP
column 4: minor allele frequency of the SNP in HapMap CEU trios
column 5: maternal genotype of 1st trio
column 6: child genotype  of 1st trio
column 7: paternal genotype of 1st trio
column 8: maternal genotype of 2nd trio
column 9: child genotype of 2nd trio
column 10: paternal genotype of 2nd trio
etc.




The same example with 5 SNPs, 10 trios:                      
10	rs1247696	29826038	0.01666667	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	
10	rs6481613	29831217	0.41666667	1	1	1	1	2	1	0	1	1	0	1	2	0	0	1	0	0	1	2	2	2	1	1	1	2	1	1	0	1	1	
10	rs2182402	29835030	0.41666667	1	1	1	1	2	1	0	1	1	0	1	2	0	0	1	0	0	1	2	2	2	1	1	1	2	1	1	0	1	1	
10	rs4747667	29840416	0.36666667	1	1	1	1	2	1	0	1	1	0	0	1	0	0	1	0	0	1	2	2	2	1	1	1	1	0	1	0	1	1	
10	rs3740003	29844044	0.25000000	1	1	1	1	1	0	1	1	1	0	0	0	0	0	0	0	0	1	1	1	2	1	1	1	1	0	1	0	1	1
 
   
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