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Old 02-04-2011, 07:54 AM   #1
libiyagirl
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Location: canada

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Default Using Dindel: callback and output on realigned BAM

Hello, when I'm using dindel, I want to output the realigned BAM file for the genome viewer. So I used the option --outputRealignedBAM, and then I had many many files. Is it possible that I merge all the realigned BAM files into one? How can I do that?
Also, I used the callback script provided by the author:
#!/bin/bash
samtools view $1 >> $2.sam
echo $3 $4 $5 >> $2.windows
rm $1
But it's not working. Any idea to improve this?

Many thanks!
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Old 02-07-2011, 06:35 AM   #2
libiyagirl
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Default

Any one has any idea?
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Old 02-10-2011, 06:53 AM   #3
Yilong Li
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Default

This is how I am running it right now. I have a file called processRealignedBams.sh, that contains the shell script you posted above.Then I am just running dindel (step 3) using the options

Code:
--outputRealignedBAM --processRealignedBAM processRealignedBams.sh
Seems to work fine with me.
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