Post date: Aug 25, 2014 5:16:18 PM
I am using samtools to sort, compress, and index the Timema genomes from Moe's project. This includes 1536 alignments. The results will be in /home/A01963476/data/timema/moe_radiation_wgrs/alignments/.
Here is an example command:
cd /home/A01963476/data/timema/moe_radiation_wgrs/alignments/
samtools view -b -S -o aln_WTCHG_135840_296.bam aln_WTCHG_135840_296.sam
samtools sort aln_WTCHG_135840_296.bam aln_WTCHG_135840_296.sorted
samtools index aln_WTCHG_135840_296.sorted.bam