Post date: Mar 01, 2014 12:1:20 AM
I created infiles for to estimate recombination rates for the merged families. Here are the commands for family 25266x25267 (the parents are #s 114 and 115). I only retained parent genotypes where the posterior probability of one genotype was at least 0.95
perl ../scripts/getParentGentoypes.pl 114 115 fam25266x25267.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.95 parentGenotypes.txt
perl ../scripts/calculateOffspringGenotypeProbs.pl 114 115 sub_parentGenotypes.txt fam25266x25267.vcf
perl ../scripts/splitP0P1.pl offspringGenotypes.txt
Here is the command for running recomb (in a jobsub file). I ran 10 replicates and only used offspring genotypes with probabilities >= 0.95. The -p 1 option prints out all of the MC replicates, which I probably don't really need to do.
cd /home/A01963476/data/timema/timema_mappingfams/mergedFam25266x25267/
recomb -i p1_offspringGenotypes.txt -o recombOutP1FA.txt -n 10 -m 0.95 -p 1
Family B, with parent ids 24 and 25:
perl ../scripts/getParentGentoypes.pl 24 25 fam25268x25269.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.95 parentGenotypes.txt
perl ../scripts/calculateOffspringGenotypeProbs.pl 24 25 sub_parentGenotypes.txt fam25268x25269.vcf
perl ../scripts/splitP0P1.pl offspringGenotypes.txt
cd /home/A01963476/data/timema/timema_mappingfams/mergedFam25268x25269/
recomb -i p1_offspringGenotypes.txt -o recombOutP1FB.txt -n 10 -m 0.95 -p 0
Family C, with parent ids 19 and 20:
perl ../scripts/getParentGentoypes.pl 19 20 fam25270x25271.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.95 parentGenotypes.txt
perl ../scripts/calculateOffspringGenotypeProbs.pl 19 20 sub_parentGenotypes.txt fam25270x25271.vcf
cd /home/A01963476/data/timema/timema_mappingfams/mergedFam25270x25271/
recomb -i p0_offspringGenotypes.txt -o recombOutP0FC.txt -n 10 -m 0.95 -p 0
My preliminary inspection of the results for family suggests that recombination rates within scaffolds are now much closer to 0, but perhaps too low to pick up meaningful variation with distance.