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Old 07-20-2010, 09:31 AM   #1
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Question sam to bam

I was sure this had been asked earlier, but could not find. Does anyone have a script to convert files from sam to bam format?

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Old 07-20-2010, 09:40 AM   #2
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Use samtools view. The -S indicates the input is in SAM format and the "b" indicates that you'd like BAM output.

samtools view -Sb  <SAMFILE>  >  <BAMFILE>
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Old 07-20-2010, 12:19 PM   #3
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You can also use samtools import command (this is what I am using), which does this exact thing.
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sam bam

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