Thank you for all your help and your great program.
I have been using LepMap3 to map SNP data from 2 full-sib families of ~300 individuals each. When I map the families separately, the markers that overlap usually map to the same linkage group (i.e. the markers that were grouped to linkage group 4 in family 1were also grouped together in linkage group 2 in family 2). However, when I combine the families for mapping in LepMap, there is less synteny compared to the 2 separated family maps. Some linkage groups are combined to a single group or separated (i.e. linkage group 1 in the combined map corresponds to linkage groups 3 and 4 in the family 1 map).
Do you know what could be causing there to be greater similarity between the separate family maps than between either separate family map and the map using the combined dataset? Should greater confidence be given to the maps with greater synteny or the map created using the larger numbr of individuals?
Any insight you have would be greatly appreicated.
Thank you,
Hayley
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Have you increased the lodLimit when combining multiple families? The grouping of two families could be more tricky as each marker can be informative only on one family. With one family or with many families the problem becomes easier. Note also that some errors in the family structure (like incorrect parents) are not visible with a single family but would show up with two families...
If you can group the markers separately for each family, it is not very difficult to combine two map files.
Providing parameter "families=FAMILY1_NAME" to SC2 with data on both famies is probably the easiest way to get started. You could even start with the grouping based on the first map and then run JoinSingles2All with both maps.
If this does not work, then you could do two map files with each family. Then you have to figure which groups correspond to which and combine the two files accordingly.
Cheers,
Pasi
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I have increased the lodLimit when combining the 2 families, so maybe my errors are arising from something else. I had a few questions about your suggestions.
I do not see the "families" paramater as an option for SC2. Would I just give the names of each family from the pedigree file? (i.e. my 2 families are names FAM1 and FAM2 in the pedigree file so families=FAM1, FAM2)?
How could I run JoinSingles2All using grouping from one map? I tried this using the SC2 file from Family 1 as the map file and the combined family data as the call file and got an error. Would this be because I have different markers in the single family call file and the combined family call file?
Finally, is combining map files something that can be done in LepMap or would I need to use another program like LPMerge?
Thank you so much for your help.
Best,
Hayley
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You need data where both families are joined together so that there is a common set of markers. If you have two single family datasets, then you have to join them on the common markers. How to do this depends on the input data format. Easiest it is if you have raw variant data and just give ParentCall2 the pedigree containing both families.
Cheers,
Pasi
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Dear Pasi,
Thank you for sharing your knowledge. I'm just starting to use Lepmap3.
My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree.
I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3?
Sorry if my question is very basic, I'm a beginner!
Thank you very much!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hi Pasi,
Thank you for all your help and your great program.
I have been using LepMap3 to map SNP data from 2 full-sib families of ~300 individuals each. When I map the families separately, the markers that overlap usually map to the same linkage group (i.e. the markers that were grouped to linkage group 4 in family 1were also grouped together in linkage group 2 in family 2). However, when I combine the families for mapping in LepMap, there is less synteny compared to the 2 separated family maps. Some linkage groups are combined to a single group or separated (i.e. linkage group 1 in the combined map corresponds to linkage groups 3 and 4 in the family 1 map).
Do you know what could be causing there to be greater similarity between the separate family maps than between either separate family map and the map using the combined dataset? Should greater confidence be given to the maps with greater synteny or the map created using the larger numbr of individuals?
Any insight you have would be greatly appreicated.
Thank you,
Hayley
Dear Hayley,
Thank you for your question.
This concerns SeparateChromosomes2 (SC2), right?
Have you increased the lodLimit when combining multiple families? The grouping of two families could be more tricky as each marker can be informative only on one family. With one family or with many families the problem becomes easier. Note also that some errors in the family structure (like incorrect parents) are not visible with a single family but would show up with two families...
If you can group the markers separately for each family, it is not very difficult to combine two map files.
Providing parameter "families=FAMILY1_NAME" to SC2 with data on both famies is probably the easiest way to get started. You could even start with the grouping based on the first map and then run JoinSingles2All with both maps.
If this does not work, then you could do two map files with each family. Then you have to figure which groups correspond to which and combine the two files accordingly.
Cheers,
Pasi
Dear Pasi,
Thank you for your response.
I have increased the lodLimit when combining the 2 families, so maybe my errors are arising from something else. I had a few questions about your suggestions.
I do not see the "families" paramater as an option for SC2. Would I just give the names of each family from the pedigree file? (i.e. my 2 families are names FAM1 and FAM2 in the pedigree file so families=FAM1, FAM2)?
How could I run JoinSingles2All using grouping from one map? I tried this using the SC2 file from Family 1 as the map file and the combined family data as the call file and got an error. Would this be because I have different markers in the single family call file and the combined family call file?
Finally, is combining map files something that can be done in LepMap or would I need to use another program like LPMerge?
Thank you so much for your help.
Best,
Hayley
Dear Hayley,
You just put families=FAM1 or FAM2, there should be parameter families is SC2, at least in my own version shows in:
You run something like this:
You need data where both families are joined together so that there is a common set of markers. If you have two single family datasets, then you have to join them on the common markers. How to do this depends on the input data format. Easiest it is if you have raw variant data and just give ParentCall2 the pedigree containing both families.
Cheers,
Pasi
Dear Pasi,
Thank you for sharing your knowledge. I'm just starting to use Lepmap3.
My goal is to create a genetic map from an F1 (fullsib population). I have some doubts about how to do it. I already have my VCF file, but not the pedigree.
I understand that I should create separate maps for each parent (mother and father), and then combine them with the offspring's map. How can I do this with LepMap3?
Sorry if my question is very basic, I'm a beginner!
Thank you very much!