Samtools - index

[Kath]

Hello,

I'm trying to use the SamTools index command. I have installed the latest version (0.1.9) but there doesn't seem to be an "index" in the SamTools folder. Instead there are "bam_index.c" and "bam_index.o". This is probably a stupid question but does anyone know the difference?

Thanks

Kath

[ntremblay]

Hi,

have you tried from your terminal, samtools index xxx.bam? this should work to index your file if you have a compiled samtools executable ...

if i'm not mistaken the bam_index.c and bam_index.o are the scripts used by your executable.

hope that helps...

Nicolas

[Kath]

Ah ha, how right you are! Thanks.