Changes

vtools select 5var --output chr pos ref alt dbNSFP.SIFT_pred dbNSFP.SIFT_score

vtools select 5var --output chr pos ref alt dbNSFP.CADD_raw dbNSFP.CADD_phred

java -jar GenomeAnalysisTK.jar --help<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T UnifiedGenotyper -glm BOTH -I child.bam -I father.bam -I mother.bam -L trio.intervals -o ug.vcf

less -S ug.vcf<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -T VariantEval -R human_g1k_v37.fa -L trio.intervals -D dbsnp.vcf -eval ug.vcf -o ug.vcf.eval<br data-attributes="%20/" />less -S ug.vcf.eval<br data-attributes="%20/" />java -Xmx200m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T SelectVariants -V ug.vcf -mv -mvq 0 -o ug.dnm.vcf -ped trio.ped<br data-attributes="%20/" />java -Xmx500m -jar GenomeAnalysisTK.jar -R human_g1k_v37.fa -T HaplotypeCaller -I child.bam -I father.bam -I mother.bam -minPruning 4 -L 1:199325670-199325672 -mergeVariantsViaLD -o hc.vcf

Data analysis:

# === Report allele frequencies after 100 generations === #<br data-attributes="%20/" />for (s in s.s) {<br data-attributes="%20/" /> cat("s=") ; cat(s) ; cat(": ")<br data-attributes="%20/" /> freqs = get(paste("freqs.s", s, sep=""))<br data-attributes="%20/" /> cat(freqs[n.gen+1]) ; cat("\n")<br data-attributes="%20/" /> }

# === Graph allele frequency changes === #<br data-attributes="%20/" />pdf("selection_plot.pdf", paper="special", height=4*2, width=4*2, onefile=F)<br data-attributes="%20/" /> plot(x=0, y=0, type="n", xlim=c(0,n.gen), ylim=c(0,1), xlab="Generation", ylab="Allele frequency")<br data-attributes="%20/" /> lines (c(0,n.gen), rep(0.5, 2), lty=3, col="#AAAAAA")<br data-attributes="%20/" /> for (s in s.s) {<br data-attributes="%20/" /> freqs = get(paste("freqs.s", s, sep=""))<br data-attributes="%20/" /> lines(0:n.gen,freqs, col="#44AAAA")<br data-attributes="%20/" /> }<br data-attributes="%20/" />dev.off()

In R: