The most frequent output of a mapper is a SAM file, but in order to process it or visualize it, I have to have a index of a sorted BAM file. I usually work with a group of alignment files, so I use a pipeline like this:

for i in $(ls *.sam)

do

name=${i%.sam}
samtools view -Sb $name.sam -o $name.bam && samtools sort $name.bam $name.sort && samtools index $name.sort.bam $name.sort.bam.bai && rm $name.sam $name.bam

done

The problem with this kind of pipeline, is that I have to use a lot of space in the disk while the pipeline is running. I know that is a way to use temporal files in the pipeline to avoid the excessive use of disk space, can you tell me how can I use temporal files insted of write and delete intermediate files (like $name.sam $name.bam)?

Thanks for your time, Cheers