Post date: Oct 01, 2014 9:36:36 PM
I am rerunning samtools view, sort and index to compress the sam files, and I am cleaning up along the way. The *sorted.bam files will be in /labs/evolution/data/timema/timema_wgrs/assembliesExperiment/. Here is an example command:
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
samtools view -b -S -o aln_4_296_66562.bam aln_4_296_66562.sam
rm aln_4_296_66562.sam
samtools sort aln_4_296_66562.bam aln_4_296_66562.sorted
rm aln_4_296_66562.bam
samtools index aln_4_296_66562.sorted.bam
Converting from sam to bam freed up quite a bit of space. Now I am using samtools to remove PCR dupilcates:
cd /home/A01963476/data/timema/timema_wgrs/assembliesExperiment/
samtools rmdup aln_0_201_52525.sorted.bam aln_0_201_52525_unique.bam
samtools index aln_0_201_52525_unique.bam
rm aln_0_201_52525.sorted.bam