Post date: Jan 04, 2014 10:30:58 PM
I am using samtools and the dorc cluster to compress, sort and index the alignments for the new mapping family data (192 alignments = 192 individuals). The sam (and soon bam) files are in data/timema/timema_mappingfams/NCGR/alignments/. Here are the commands for one individual:
cd /home/A01963476/data/timema/timema_mappingfams/NCGR/alignments/
samtools view -b -S -o alnMAP25300.bam alnMAP25300.sam
samtools sort alnMAP25300.bam alnMAP25300.sorted
samtools index alnMAP25300.sorted.bam