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Old 11-24-2010, 08:43 AM   #1
Kath
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Location: Oxford

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Default Samtools - index

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
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Old 11-24-2010, 08:52 AM   #2
ntremblay
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Default

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
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Old 11-24-2010, 09:06 AM   #3
Kath
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Ah ha, how right you are! Thanks.
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