Post date: Sep 21, 2015 6:34:10 PM
I think I have the extractGeneticData.pl script working. It grabs the haplotypes and quality scores for each individual and read contained with a haplotype locus. The key output is hapdata.txt. The script is running now:
reuse SAMtools
cd /home/A01963476/data/aspen/gbs/Assemblies/
perl Scripts/extractGeneticData.pl noindel*.sorted.sorted.bam