sam to bam then delete sam file

Question

[houssienali]

Hi, how can I make a loop for sam to bam then delete sam file in the same loop

[swbarnes2]

Are you sure you can't pipe your output straight to something that will convert it to bam? For instance, samtools sort will work on a sam, so you can pipe your sam output straight into it, and never actually make a sam file.

[Pierre Lindenbaum]

what did you try ?

Answer 1

[seidel]

As others have suggested, do you have a process that generates SAM output that can be piped directly to samtools?

# sam output generated, yet sam file never exists
bowtie alignment_index -c GGATCC --sam | samtools view -b -o output.bam -

What language/method would you like to loop with? What have you tried? A bash example:

#!/bin/bash

sam_file="my_filename.sam"
alignment_index="path_to_your_index"

for f in $sam_file
do
  bowtie $alignment_index -c GGATCC --sam > $f
  samtools view $f -b -o output.bam
  rm $f
done