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Old 02-04-2011, 08:54 AM   #1
Location: canada

Join Date: Jan 2011
Posts: 27
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:
samtools view $1 >> $2.sam
echo $3 $4 $5 >> $
rm $1
But it's not working. Any idea to improve this?

Many thanks!
libiyagirl is offline   Reply With Quote
Old 02-07-2011, 07:35 AM   #2
Location: canada

Join Date: Jan 2011
Posts: 27

Any one has any idea?
libiyagirl is offline   Reply With Quote
Old 02-10-2011, 07:53 AM   #3
Yilong Li
Location: WTSI

Join Date: Dec 2010
Posts: 41

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

--outputRealignedBAM --processRealignedBAM
Seems to work fine with me.
Yilong Li is offline   Reply With Quote


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