Some issues with the Populations Joinmap output

[Ira Herniter]

Hi,

I'm trying to export my Populations output as a Joinmap input to do some map construction. I've run into a few problems, however.

I used this command to get the output:

• $ populations -V ./16-5/vcf/16-5_chr.vcf --popmap popmap_16-5_joinmap.tsv --out-path ./16-5/joinmap --min-maf 0.2 --min-samples-per-pop 0.90 --map-type CP --map-format joinmap
  

It successfully created a .loc file, but when I attempted to input it into Joinmap (v5), I got the error: 

• no "data type" statement in mapmaker (?) file

When I looked into the .loc file I found that it used # instead of ; to note null lines, so I changed those. When I tried to import the modified file, I got this error:

• unable to determine type of data in the file

I also noted in the .loc output file that it did not keep the marker physical location (chromosome or bp) or name, just giving me the marker number, which means it will be rather more difficult to line up the genotype and map. Are there options I should have selected to keep the marker information and does something need to be done to the .loc to make sure it can be imported?

Thanks,

Ira

[Catchen, Julian]

Hi Ira,

 

The assumed use case for mapping is that you are doing a de novo analysis of RAD data to build a genetic map independent of any reference genome, so the exporting code does not make an effort to export reference coordinates. The program is not really designed as a format converter from a VCF file. It may work for this, but it is not a case we test…

 

Anyway, do you actually get useable markers out of the dataset, prior to trying to import into JoinMap? Also, are you specifying the right kind of import? Joinmap does use Mapmaker format for F2s and some other maps, but not for CP maps, if I remember correctly. Many CP marker types would require more than one SNP per locus (as you would get in a RAD analysis but not in a SNP-only analysis).

 

Best,

 

juilan

[Joshua Havill]

Hi Ira,

In this case, you could change the '.loc' file to '.loc.txt' and open the file in Excel. From here you can open up JoinMap and 'Create Datasheet' and specify the number of individuals and the number of markers present in the data matrix. You will need to leave the phase column blank, meaning the marker name and segregation type should be copied and pasted together, along with copying and pasting the genotypes (individual names) and markers together.

You can then choose to 'Create Population Node' or "Create Maternal/Paternal Nodes', depending on what you're trying to accomplish.

Cheers,

Josh

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[Ira Herniter]

Hi,

I was able to import the data into Joinmap by copying and pasting, so that was fine. However, I ran into another problem, which is that populations filters out markers for which it cannot determine a parental genotype. This would be fine, other than that it also recovers some number of the parental genotypes.

The info from the terminal is in the attached image file.

My issue is that it won't tell me which markers were removed. None of the log or summary files seem to contain this information. I know you said that the assumption was that the Joinmap output is a de novo mapping, but I need to do some additional filtering using r/QTL, and I also cannot use the Joinmap format for marker-trait association, so I either need to be able to know which markers are being removed by populations or I need to be able to convert the Joinmap format back to AB format.

Thanks,

Ira

[Catchen, Julian]

Hi Ira,

 

Sorry, but it is not entirely clear to me what you need from the output of Stacks for your mapping analysis. However, can you just compare the markers that are in the VCF (or sumstats file) with those that are in the Joinmap export? The marker IDs are consistent across populations runs, so you can make a list with some grep commands of what is in one file but not the other (I’m not sure how you would use this info, so perhaps my suggestion is not useful).

 

julian