Converting SAM directly to a sorted BAM file
Like many Unix tools, SAMTools is able to read directly from a stream i.e. stdout.
samtools
samtools view -bS file.sam | samtools sort - file_sorted
1440 samtools view -bS DPB1_13\:01.report.bowtie2.sam | samtools sort - DPB1_13_01
1442 samtools index DPB1_13_01.bam DPB1_13_01.bai
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