I was hoping to try out Lep-Map3, but I'm not sure what the input format is. Is it the same as previous versions? Are you planning any documentation soon? Thanks for creating this software!
Kind Regards,
Kris Christensen
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The (genotypic) input format is identical to of ParentCall of LM2. That is, markers are on lines, columns 1+2 are CHR and POS and 6 first lines consist of the pedigree information.
Sorry for delay, I should finalize a manuscript and documentation soon for LM3.
Cheers,
Pasi
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The first 6 lines are identical to 6 first columns (in transpose), expect you have to add "CHR" and "POS" as the first two columns in LM3 format to match columns of the data and pedigree.
Hi Pasi,
What if the values under CHR or POS for every marker are not known?
Also, the genotypes can be written in the same way as the pre-makeped linkage format?
Thank you !
-BQ
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The actual "CHR POS" columns are not important as they are not used for anything but there must be two columns in the begining of each line. You can actually have "CHR\tPOS" for every marker and pedigree...
The genotypes have to be converted to Lep-MAP format, if the numeric values are between 1..4 you can used linkage2post.awk provided with Lep-MAP2.
Cheers,
Pasi
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello Pasi,
I was hoping to try out Lep-Map3, but I'm not sure what the input format is. Is it the same as previous versions? Are you planning any documentation soon? Thanks for creating this software!
Kind Regards,
Kris Christensen
Dear Kris,
The (genotypic) input format is identical to of ParentCall of LM2. That is, markers are on lines, columns 1+2 are CHR and POS and 6 first lines consist of the pedigree information.
Sorry for delay, I should finalize a manuscript and documentation soon for LM3.
Cheers,
Pasi
Hello Pasi,
Just to confirm, the first 6 lines of pedigree information are similar to the first 6 columns of the pre-makeped linkage format?
cheers,
Pragya
Hello Pragya,
The first 6 lines are identical to 6 first columns (in transpose), expect you have to add "CHR" and "POS" as the first two columns in LM3 format to match columns of the data and pedigree.
linkage:
F 1 0 0 2 0
=>
posterior:
CHR POS F
CHR POS 1
CHR POS 0
CHR POS 0
CHR POS 2
CHR POS 0
and all tab separated.
Cheers,
Pasi
Last edit: Pasi Rastas 2017-01-24
Hi Pasi,
What if the values under CHR or POS for every marker are not known?
Also, the genotypes can be written in the same way as the pre-makeped linkage format?
Thank you !
-BQ
Dear BQ,
Thanks for the question.
The actual "CHR POS" columns are not important as they are not used for anything but there must be two columns in the begining of each line. You can actually have "CHR\tPOS" for every marker and pedigree...
The genotypes have to be converted to Lep-MAP format, if the numeric values are between 1..4 you can used linkage2post.awk provided with Lep-MAP2.
Cheers,
Pasi