Map types in genotypes program in Stacks

[Anupriya Verma]

Hi all,

Can anyone tell me what are different types of crosses we can give in 'genotypes program' ? According to manual it can be included by giving '-t' option. 'CP', 'DH', 'F2', 'BC1' and 'GEN' are the currently supported map types. What do these abbreviation means?

Thanks in advance!

[Julian Catchen]

Hi Anupriya,

The GEN format is generic, all markers are reported. This is useful if you want to do your own encoding after exporting. The other types are defined in a number of places, here is Table 1 from the JoinMap manual (https://www.kyazma.nl/docs/JM4manual.pdf):



Best,

julian

Anupriya Verma

March 23, 2017 at 11:23 PM

[ido bar]

Hi Julian,

Regarding this topic, how would you export the results from genotypes module for a F5 RIL cross map? (the equivalent to RI5 from the table you've attached) 

I've tried specifying it, but Stacks only accepts the following: 'CP', 'DH', 'F2', 'BC1', and 'GEN' (according to the manual).

I'm intending to export the results to OneMap, which supports the following (should be the same as MapMaker):

Thanks, Ido

[Darwin Pinzón]

I'm also interested in this question. I have F4 RILs (from sibling matings) so "IM4F0" not RI4.