import reference.fa reference in samtool ubuntu

[scibetta]

Hello everybody,
I am very new with samtool. I need to convert a sam file generated with bowtie into bam. I need some help from scratch (all the commands in ubuntu to be used) on how to import and index the hg.19.fa reference file from bowtie or internet.
Please please please help me.
Angelo

[swbarnes2]

I need to convert a sam file generated with bowtie into bam.

samtools view -bhS yourfile.sam > yourfile.bam

Poke around the Bowtie site, you can probably find a pre-indexed hg19 that you can just download, since it's a popular genome.