Sib-pair Command: test strand

Class	Analysis and data manipulation command
Name	test strand
Arguments	[<marker 1> [...<marker N>]].

Test if mix of genotypes for a locus are compatible with a strand mixup.

Example:

set loc snp1 snp 1:1
set loc snp2 snp 1:2
read cases inline
1 A/A A/C
2 C/C C/C
3 A/C C/C
4 T/G C/T
;;;;
run

>> write

Mean size of pedigrees     =          1.0
# Writing 4 pedigrees:
!  i f m s                
!  d a o e                
!    t t x  snp1    snp2  
!
1 1 x x  x   A/A     A/C  
2 2 x x  x   C/C     C/C  
3 3 x x  x   A/C     C/C  
4 4 x x  x   G/T     C/T  

>> set plevel 2

NOTE:  Print level  2


>> test strand                                                                


Locus          Alleles   HWE P      Action
-------------- --------- --------- ----------
snp1             AC  GT    0.3985  Recoding "snp1" A C to T G

>> wri                                                                        

# Writing 4 pedigrees:
!  i f m s                
!  d a o e                
!    t t x  snp1    snp2  
!
1 1 x x  x   T/T     A/C  
2 2 x x  x   G/G     C/C  
3 3 x x  x   G/T     C/C  
4 4 x x  x   G/T     C/T