Post date: Nov 19, 2014 5:24:24 PM
rsync failed to transfer the piMASS results, because the file glob was not interpreted correctly. While trying to solve this I accidently deleted the gemma/piMASS infiles. Now I am re-making them (and making better notes of how I do this).
1. Create the genotype row header file. From /home/A01963476/projects/timema_wgexperiment/variants/ run:
cat filtered_variantsLG*vcf | grep ^lg | cut -f 1,2,4,5 | perl -p -i -e 's/\s+/-/' | perl -p -i -e 's/\s+(\S+)/, \1/g' > ../gemma/genRowHdr.txt
2. Make the genotype files. From the gemma subdirectory run,
perl scripts/mkGemma.pl
3. Make the phenotype files. Also from the gemma subdirectory,
perl scripts/mkPheno.pl samples
4. Make the annotation file,
cp genRowHdr.txt annotation.txt
perl -p -i -e 's/^(lg\d+_ord\d+_scaf)(\d+)\-(\d+),\s+[ATCG],\s+[ATCG]/\1\2-\3, \2, \3/' annotation.txt