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Old 01-28-2011, 01:51 PM   #1
libiyagirl
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Default another stupid question about dindel

Hello, I'm running the stage 3 of dindel now. On stage 2 it generated hundreds realign_window.n.txt files. Does it mean I have to run all of them on stage 3 to get hundreds of the output_windows.glf.txt files?

Also when I merge the files on stage 4, it says warning: file msg does not exist! what does this mean?
Thank you!
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Old 01-28-2011, 05:31 PM   #2
gaffa
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That's correct, you run "dindel --analysis indels" once for each file (if you know a bit of shell-scripting you can easily automate this), and it generates one output file per input file.

Regarding stage 4, see this thread for some discussion: http://seqanswers.com/forums/showthread.php?t=8301
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Old 01-31-2011, 08:00 AM   #3
libiyagirl
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hi gaffa,

thank you very much for your reply. however, regarding stage 4, the problem is still not solved. so I created a file run1_outputfiles.txt, with the following lines:

/path/sample_output_windows.1.glf.txt
/path/sample_output_windows.2.glf.txt
/path/sample_output_windows.3.glf.txt
.......

Then in unix, I typed
python mergeOutputDiploid.py --inputFiles /path/run1_outputfiles.txt \--outputFile variantCalls.VCF --ref /path/ref.fa

but it is telling me File /path/sample_output_windows.1.glf.txt does not exit.
.Aborting.
An error occurred!

I'm so confused. Did I miss anything?

Thank you so much for your help!
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Old 01-31-2011, 08:24 AM   #4
libiyagirl
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Hello, problem solved! It was funny because I basically typed the same thing! But this time it's working. Big thanks!
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Old 03-10-2011, 04:25 AM   #5
colindaven
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Default Automating dindel stage 3

If it s helpful to any non-coders, I wrote a mini perl script to batch analyse all the windows.
Just change the number of windows to reflect the number you made. You'll need to change the file names etc in the command line too of course.

Code:
#!/usr/bin/perl

$i = 1;
$no_of_windows = 44;

while ($i <= $no_of_windows) {
	
	`dindel-1.01-linux-64bit --analysis indels --doDiploid --bamFile ../TB_stampy_sorted.bam --ref NC_002516.fa --varFile windows/TB.realign_windows.$i.txt --libFile TB.dindel.libraries.txt --outputFile TB.realign_output.windows.$i.txt`;
	$i = $i + 1;
}

Last edited by colindaven; 03-10-2011 at 04:29 AM.
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Old 07-30-2012, 02:06 AM   #6
clarissaboschi
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Hi! I was trying to use your perl script but did not work. I am not vey good in perl, so could be my mistake. But I changed the file names and the number of windows, which in my case is 78.
I had the error message

Global symbol "$i" requires explicit package name at dindel.pl line 4.
Global symbol "$no_of_windows" requires explicit package name at dindel.pl line 5.
Global symbol "$i" requires explicit package name at dindel.pl line 7.
Global symbol "$no_of_windows" requires explicit package name at dindel.pl line 7.
Global symbol "$i" requires explicit package name at dindel.pl line 9.
Global symbol "$i" requires explicit package name at dindel.pl line 9.
Global symbol "$i" requires explicit package name at dindel.pl line 10.
Global symbol "$i" requires explicit package name at dindel.pl line 10.
Execution of dindel.pl aborted due to compilation errors.

What could be the error?
Thanks
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Old 07-30-2012, 04:03 AM   #7
colindaven
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Hi Clarissa,

I wouldn't recommend Dindel at all, we did not get anything out of it at all.

But if you want to keep trying, it seems your perl installation requires strictly defined variables by default.

Try this
my($i) = 1;
my($no_of_windows) = 44;
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Old 07-30-2012, 07:38 AM   #8
clarissaboschi
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Thanks, I changed the script and it is working now.
But why do you not recommend Dindel??
I trying to identify indels, and I used before Samtools/mpileup, but some people say that Dindel is better, so I am currently running some analysis to see the differences with Samtools.

Thanks
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