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Old 12-09-2016, 02:03 PM   #9
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Location: Wellington, NZ

Join Date: Dec 2016
Posts: 4

Originally Posted by Brian Bushnell View Post simply calls Samtools with the correct (or, in the above case, apparently incorrect) commands to produce a sorted, indexed bam file.
Hi Brian,

Would you say that the problem comes from the missing output option?
If so, do you know how to fix that error?

If that helps, it may also be related to the samtools version, I'm using version 1.3 and when executing the script, the module commands on line 2 and 3 of did not work (command not found error, which I don't understand why so far).

I'm re-running the whole job with samtools 0.1.19, I'll post the outcome here.
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