Post date: Apr 15, 2016 11:1:43 PM
Recombination rate estimates by family (P1 appears to be female informative, NEED TO CHECK THIS?).
Families with one possible father:
perl ../scripts/getParentGentoypes.pl 0 1 filtered2x_fam123.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam123.txt
##Found 447 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs.pl 0 1 sub_parentGenotypes_filtered2x_fam123.txt filtered2x_fam123.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam123.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam123.txt -o rp0fam123 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam123.txt -o rp1fam123 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.000000 0.000000 0.000000 0.002579 0.002000 0.254000
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.000000 0.000000 0.001000 0.005016 0.003000 0.332000
perl ../scripts/getParentGentoypes.pl 0 1 filtered2x_fam143.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam143.txt
##Found 12090 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs.pl 0 1 sub_parentGenotypes_filtered2x_fam143.txt filtered2x_fam143.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam143.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam143.txt -o rp0fam143 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam143.txt -o rp1fam143 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# 0.0000 0.0180 0.0840 0.1172 0.1860 0.5000
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00800 0.04700 0.09577 0.14800 0.50000
perl ../scripts/getParentGentoypes.pl 0 1 filtered2x_fam297.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam297.txt
##Found 118 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs.pl 0 1 sub_parentGenotypes_filtered2x_fam297.txt filtered2x_fam297.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam297.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam297.txt -o rp0fam297 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam297.txt -o rp1fam297 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00000 0.00200 0.01061 0.00700 0.36300
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00000 0.00000 0.01568 0.00400 0.29700
perl ../scripts/getParentGentoypes.pl 0 1 filtered2x_fam309.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam309.txt
## Found 155 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs.pl 0 1 sub_parentGenotypes_filtered2x_fam309.txt filtered2x_fam309.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam309.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam309.txt -o rp0fam309 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam309.txt -o rp1fam309 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00000 0.00000 0.01917 0.01600 0.50000
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00000 0.00000 0.01925 0.02500 0.28700
Families with 2 possible fathers ("real" father chosen to minimize segregation distortion; median across loci), two families (f26, f181, f287) with median seg. distortion p-values always equal to 0.00000 were dropped because it was hard to say who the father was:
## male 273 (matches my previous guess)
perl ../scripts/getParentGentoypes.pl 0 1 filtered2x_fam272.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam272.txt
## Found 1917 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs2.pl 0 1 2 sub_parentGenotypes_filtered2x_fam272.txt filtered2x_fam272.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam272.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam272.txt -o rp0fam272 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam272.txt -o rp1fam272 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00000 0.00500 0.06203 0.09300 0.50000
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
# 0.0000 0.0010 0.0300 0.1077 0.2120 0.5000
## male 202 (matches my previous, uncertain, guess)
perl ../scripts/getParentGentoypes.pl 0 2 filtered2x_fam200.vcf
perl ../scripts/thresholdParentGenotypes.pl 0.9 parentGenotypes_filtered2x_fam200.txt
## Found 14226 recombination informative loci
perl ../scripts/calculateOffspringGenotypeProbs2.pl 0 2 1 sub_parentGenotypes_filtered2x_fam200.txt filtered2x_fam200.vcf
perl ../scripts/splitP0P1.pl sub_offspringGenotypes_filtered2x_fam200.txt
recomb -i p0_sub_offspringGenotypes_filtered2x_fam200.txt -o rp0fam200 -n 10 -m 0.9 -p 0
recomb -i p1_sub_offspringGenotypes_filtered2x_fam200.txt -o rp1fam200 -n 10 -m 0.9 -p 0
## distribution of binomial probs for seg distortion
summary(x0[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.01000 0.05400 0.09943 0.16200 0.50000
summary(x1[,6])
# Min. 1st Qu. Median Mean 3rd Qu. Max.
#0.00000 0.00800 0.04900 0.09361 0.14800 0.50000
Lycaeides has 24 (or maybe 23) chromosomes (Robinson, 1971; search for Lycaeides).