Post date: May 07, 2014 8:33:35 PM
I used samtools to compress, sort and index the genomes from the within generation experiment described in the Ecology Letters paper. There are 1986 alignments total, and here is one example set of command.
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
samtools view -b -S -o aln_4_296_66562.bam aln_4_296_66562.sam
samtools sort aln_4_296_66562.bam aln_4_296_66562.sorted
samtools index aln_4_296_66562.sorted.bam
Next I need to re-name and merge these (the script for this is ready to go and there is a file, indIds.txt with the name conversions).