sorting bowtie2 results using samtools sort

Question

[ggman]

Greetings friends,

I have successfully ran bowtie2 on my file and I am having trouble sorting my data based on a genome file that I have genome.fa.fai

It appears samtools does not use import anymore so I do not know how to go about using this file as a reference. This is the command I have been trying to use.

samtools import ~/genome_data/ref_genome.fa.fai - - | samtools sort - bowtie_run.pair

I am going to eventually merge the files, which I do not have a problem with but the command above is giving me trouble when running it through a shell script, bowtie2 is running successfully so I am almost certain that is not the problem.

[ggman]

 import    samtools import <in.ref_list> <in.sam> <out.bam>

                 Since 0.1.4, this command is an alias of:

                 samtools view -bt <in.ref_list> -o <out.bam> <in.sam>

[Pierre Lindenbaum]

what is samtools import ?

[ggman]

it ran on an older version of samtools at some point or something like that. Actually... I think I found a solution....

 import    samtools import <in.ref_list> <in.sam> <out.bam>

                 Since 0.1.4, this command is an alias of:

                 samtools view -bt <in.ref_list> -o <out.bam> <in.sam>

can be found here