SimWalk2 format conversion

[Nandita Mukhopadhyay]

The latest version leaves genotypes as A/C/T/G when converting from Plink PED files. Is there a version of SimWalk2 that can handle letter alleles? The existing version 2.91 doesn't appear to be able to.

Thanks,

Nandita

[Dan Weeks]

Thank you for letting us know of this new problem, which we will investigate and fix.

In the meantime, the flag, —force_numeric_alleles  (with two dashes at the beginning) does what it says and should make things work for you if SimWalk2 version 2.91 does not allow letter alleles.

[Dan Weeks]

SimWalk2 can handle letter alleles.

If I take the example ‘bed.*’ files from the ‘example’ directory of the Mega2 distribution, 

bed.bed bed.bim bed.fam

and change the bim  file to look like this:

$ cat bed.bim

5       M1      0       1       A       T

5       M3      5       2       G       C

5       M2      8       3       C       G

and then convert to SimWalk2 format using Mega2 v4.8.0, the resulting files contain letter alleles

$ head sw2_pedigree.05 

(I5,1x,A3)

(3A4,1X,2A1,(T16,3(A8),:))

   11   1

   1         M           A/  T   G/  C 

                 C/  C         

   2         F           A/  T   C/  C 

                 G/  G         

   3         M           T/  T   G/  C 

                 C/  G         

   4   1   2 F           A/  T   G/  C 

and run just fine though SimWalk2.

So we are not able to reproduce your problem in our hands?