Is there an easy way to convert a set of SNPs (in hapmap or vcf format) into a genotype file that could be used by something like R/qtl?
By a genotype file I mean something where columns are markers, rows are different lines, and the data is coded as either A (parent 1), B (parent 2), or H (het):
marker1 marker2
parent1 A A
parent2 B B
line1 A B
line2 B A
line3 H A
I do have the calls for each parent.. but these are different than the reference that was used to generate the hapmap/vcf files.
Seems like I could write a script to do this, or use excel, but surely there is a tool out there for this sort of thing?
Thanks!
By a genotype file I mean something where columns are markers, rows are different lines, and the data is coded as either A (parent 1), B (parent 2), or H (het):
marker1 marker2
parent1 A A
parent2 B B
line1 A B
line2 B A
line3 H A
I do have the calls for each parent.. but these are different than the reference that was used to generate the hapmap/vcf files.
Seems like I could write a script to do this, or use excel, but surely there is a tool out there for this sort of thing?
Thanks!