This is a long-ish post so I'll just start by saying that while I can get the example data set to run with ParentCall2, when I try to run it with my own data it just exits with an error 504 message. I am confident the structure of my input file is correct, but I'm worried that I'm specifying things in a way that doesn't make sense because the design of my experiment may not work with this program.
I'm working on a project in which we have relatively low sampling of individuals and I'm trying to make the best of what we have on hand. I have targeted sequence capture data for 96 individuals, 24 males and 24 females, as well as 48 half-sibs from one of the (known) females. The goal of the project is to map the sex determination region in this non-model plant. I know the mother, because I know which plant the fruit was attached to, but the father may be among the sampled plants, or may not be one of the plants I've sampled.
I've already used an Fst outlier analysis to identify the regions associated with the greatest differences between the sexes. However, this is based on an alignment of the sequence capture data to a reference genome from a different species. I was hoping to get a rough, unordered linkage map to see what other markers my sex-linked markers are associated with.
So I followed the mpileup -> input file directions from the wiki, and generated a pedigree file by hand. These data only include the genotyped mother, as well as the 48 half-sibs. In the pedigree file I specify that all the half-sibs have the same mother (1) in this case, and no father (0). I suspect that this is the reason that I'm getting an uninformative error message about the input file.
Is it possible to run lep-map with the data that I have? Or should I look for a different program? The documentation suggests that it can impute missing genotypes, but perhaps having NO paternal information is too extreme a case?
Thanks!
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Indeed, you have to specify both parents even you do not have any data on them. So just add dummy individual(s) to you pedigree that are the missing parents of your families.
If you provide the posteriorFile (or vcfFile) to ParentCall2 then you just add the dummy parents to the pedigree (ParentCall2 will give a warning about not having data, just ignore this). If you create full data manually, you have to add missing data "1 1 1 1 1 1 1 1 1 1" (actually "1" suffices) for the genotype of the dummy individual(s).
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
So, does it means I have to split the Run mpileup + pileupParser2 + pileup2posterior pipe file? I generate it with mpileup, then add the missing parents with 1s and run the pileupParser2 + pileup2posterior?
F
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I thing my pedigree.txt is not well formatted. Would you please check it. As soon as the pedigree.txt contains the F2 family I got the error. And if I put F1 in all fields I get Error: Too many parents in a family F1
Please help
F
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
How? And, according to the other thread, which would be the parameters to
be more of less stringent, especially in the filtering process.
Now it's running the last step with no errors. I'll then just need to
figure out how to convert it for AllMaps
###### Thu 4 Apr 10:33:45 BST 2019: 2. Run ParentCall2
No grandparents present in family F1
Warning: Different number of grandparents (0 and 2) in family F2
Found 2 grandparents in family F2
Number of individuals = 88
Number of families = 2
Hello,
This is a long-ish post so I'll just start by saying that while I can get the example data set to run with ParentCall2, when I try to run it with my own data it just exits with an error 504 message. I am confident the structure of my input file is correct, but I'm worried that I'm specifying things in a way that doesn't make sense because the design of my experiment may not work with this program.
I'm working on a project in which we have relatively low sampling of individuals and I'm trying to make the best of what we have on hand. I have targeted sequence capture data for 96 individuals, 24 males and 24 females, as well as 48 half-sibs from one of the (known) females. The goal of the project is to map the sex determination region in this non-model plant. I know the mother, because I know which plant the fruit was attached to, but the father may be among the sampled plants, or may not be one of the plants I've sampled.
I've already used an Fst outlier analysis to identify the regions associated with the greatest differences between the sexes. However, this is based on an alignment of the sequence capture data to a reference genome from a different species. I was hoping to get a rough, unordered linkage map to see what other markers my sex-linked markers are associated with.
So I followed the mpileup -> input file directions from the wiki, and generated a pedigree file by hand. These data only include the genotyped mother, as well as the 48 half-sibs. In the pedigree file I specify that all the half-sibs have the same mother (1) in this case, and no father (0). I suspect that this is the reason that I'm getting an uninformative error message about the input file.
Is it possible to run lep-map with the data that I have? Or should I look for a different program? The documentation suggests that it can impute missing genotypes, but perhaps having NO paternal information is too extreme a case?
Thanks!
Dear Brian,
Thank you for your question.
Indeed, you have to specify both parents even you do not have any data on them. So just add dummy individual(s) to you pedigree that are the missing parents of your families.
If you provide the posteriorFile (or vcfFile) to ParentCall2 then you just add the dummy parents to the pedigree (ParentCall2 will give a warning about not having data, just ignore this). If you create full data manually, you have to add missing data "1 1 1 1 1 1 1 1 1 1" (actually "1" suffices) for the genotype of the dummy individual(s).
Cheers,
Pasi
Hi Pasi,
So, does it means I have to split the
Run mpileup + pileupParser2 + pileup2posteriorpipe file? I generate it withmpileup, then add the missing parents with 1s and run thepileupParser2 + pileup2posterior?F
Hi Pasi,
I thing my
pedigree.txtis not well formatted. Would you please check it. As soon as the pedigree.txt contains theF2family I got the error. And if I putF1in all fields I getError: Too many parents in a family F1Please help
F
Here the pedigree file and the pedigree tree
F
Dear Francesco,
The problem is that in your pedigree, family F2 does not have parents. Here is a corrected version.
And to add, you do not have to split anything or run mpileup for multiple times.
Cheers,
Pasi
Last edit: Pasi Rastas 2019-04-01
Ok, now I see. I thought I needed to keep the parents of the F2 parents.
Great! Now I'll give it a try!
Thanks a lot
F
Now it says
by actually grandparents for family F2 exists!
F
Yes,
You can just add the grandparents to the pedigree for corresponding families and parents.
Cheers,
Pasi
How? And, according to the other thread, which would be the parameters to
be more of less stringent, especially in the filtering process.
Now it's running the last step with no errors. I'll then just need to
figure out how to convert it for AllMaps
Thanks a lot!!!
F
On Tue, 2 Apr 2019, 07:51 Pasi Rastas, lep-map@users.sourceforge.net
wrote:
Searching for "grandparents" :)
https://sourceforge.net/p/lep-map3/discussion/general/thread/885598e615/
Is this log means that I did it right?
F
Il giorno mer 3 apr 2019 alle ore 08:43 Pasi Rastas lep-map@users.sourceforge.net ha scritto:
Last edit: Francesco Cicconardi 2019-04-04
Seems ok,
Cheers,
Pasi
Shell I run everything with default parameters? How many iterations for
ordermarkers2?
F
On Thu, 4 Apr 2019, 11:36 Pasi Rastas, lep-map@users.sourceforge.net
wrote: