Conversion of Bowtie and Sam format alignment files

Question

I need both my alignment files to be in both bowtie and samtools format so that I can feed them into different programs later on in my pipeline. Is there any method I can use to convert a sam alignment file into a bowtie alignment file and vice versa?

An alternative would be to do the alignment twice and get the bowtie program to output it in different formats in each case. However, this wastes too much time.

Answer 1

I don't know a specific method, but I would get SAM from bowtie and then convert to bowtie format since SAM has all the information. You can do it with simple command linux with awk.