Microsat allele lengths?

[Jean]

Hi everyone,

Some summary statistics computed by PopABC use the length of microsat
alleles (varL,kurL). But nowhere in the data file specification (.len)
do I see any mention of allele lengths.
How do I encode allele lengths in my genetic data?

Thanks for your help.

Jean

[Joao Sollari Lopes]

Hi Jean,

The allele length in the table files (.len) is specified as the index of the various alleles.
Here is an example taken from toytable.len:

6
   2    5    1    1    0    0
   0    1    0    0    5    5

   6    7    8    9   10   11

The first number represents the number of different alleles (in this cases is 6) The following two lines represent the frequency of each allele in the two population considered (one line for each population). And the final line represents the length of each allele (6, 7, 8, 9, 10 and 11).
Note that the length of the alleles is considered as the number of repetitions. So, in the case of:
CAACAACAACAA
the length should be 4.

In the case of sequence data, instead of a final line representing the length of the alleles, there is a line with indexes (0, 1, 2,...). Then there is an extra line with the number of considered sites in the sequence and a legend relating each index with its own snp pattern.

Joao