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Old 11-09-2011, 10:18 AM   #1
ardmore
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Default Can I view output the entire genome data?

Suppose I have a sam file?
Can I use samtools command to get whole genome data?

Thanks.
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Old 11-09-2011, 11:49 AM   #2
dpryan
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Could you describe what "whole genome data" means?
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Old 11-09-2011, 11:51 AM   #3
ardmore
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If we use samtools, we can select chromosome.
The entire means from chr1 to chr 23.
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Old 11-09-2011, 11:57 AM   #4
swbarnes2
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By default, samtools view will convert the whole .sam file into a .bam. Just don't add a chromosome name to the command line, and you'll get everything.
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Old 11-09-2011, 01:07 PM   #5
ardmore
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Can we identify the start and the end position?
I just guess that start from 0 and end with a big number.
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Old 11-09-2011, 01:12 PM   #6
dpryan
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If you want the whole thing then don't add start or end positions. From reading the man page, I gather that specifying start and end positions without indicating an actual chromosome would confuse things.

Last edited by dpryan; 11-09-2011 at 01:13 PM. Reason: I should really proof read before hitting post...
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Old 11-09-2011, 01:21 PM   #7
jbrwn
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to get everything just:
Code:
samtools view .bam
to get everything and the header:
Code:
samtools view -h .bam
for .sam, add the sam option
Code:
samtools view -S .sam
however, if you did want to make selections from the sam:
Code:
samtools view -S .sam chr1:0-1000000
will grab reads that meet the criteria of being on chr1 between 0 and 1000000 (inclusive)

Last edited by jbrwn; 11-09-2011 at 01:24 PM.
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