View Single Post
Old 12-09-2016, 02:03 PM   #9
antoinefelden
Junior Member
 
Location: Wellington, NZ

Join Date: Dec 2016
Posts: 4
Default

Quote:
Originally Posted by Brian Bushnell View Post
bs.sh 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 bs.sh, the module commands on line 2 and 3 of bs.sh 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.
antoinefelden is offline   Reply With Quote