Using Dindel: callback and output on realigned BAM

libiyagirl · 02-04-2011, 08:54 AM

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!

libiyagirl · 02-07-2011, 07:35 AM

Any one has any idea?

Yilong Li · 02-10-2011, 07:53 AM

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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02-04-2011, 08:54 AM	#1
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	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!

02-10-2011, 07:53 AM	#3
Yilong Li Member Location: WTSI Join Date: Dec 2010 Posts: 41	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.

02-07-2011, 07:35 AM	#2
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Any one has any idea?