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Old 06-29-2010, 02:57 PM   #1
thinkRNA
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Default convert BAM -> SAM?

how can one convert from BAM to SAM
I can use samtools to go from SAM to BAM but not other way. samtools only outputs BAM format, does anyone know? Thanks in advance!
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Old 06-29-2010, 04:58 PM   #2
lvaruzza
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samtools -b -S in.sam > out.bam
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Old 06-29-2010, 08:56 PM   #3
thinkRNA
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Quote:
Originally Posted by lvaruzza View Post
samtools -b -S in.sam > out.bam
is this not sam to bam? I want to go the other way (bam to sam). thanks!
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Old 06-29-2010, 09:51 PM   #4
zee
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Read the samtools manual page at http://samtools.sourceforge.net/samtools.shtml

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samtools view in.bam > out.bam
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Old 06-30-2010, 03:08 AM   #5
Daniel Su
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Quote:
Originally Posted by zee View Post
Read the samtools manual page at http://samtools.sourceforge.net/samtools.shtml
Thank you zee.
By the way, the header section would be absent.

Last edited by Daniel Su; 06-30-2010 at 03:14 AM.
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