Can I view output the entire genome data?

ardmore · 11-09-2011, 10:18 AM

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

Thanks.

dpryan · 11-09-2011, 11:49 AM

Could you describe what "whole genome data" means?

ardmore · 11-09-2011, 11:51 AM

If we use samtools, we can select chromosome.
The entire means from chr1 to chr 23.

swbarnes2 · 11-09-2011, 11:57 AM

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.

ardmore · 11-09-2011, 01:07 PM

Can we identify the start and the end position?
I just guess that start from 0 and end with a big number.

dpryan · 11-09-2011, 01:12 PM

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.

jbrwn · 11-09-2011, 01:21 PM

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)

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11-09-2011, 10:18 AM	#1
ardmore Member Location: USA Join Date: Jun 2011 Posts: 51	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.

11-09-2011, 01:12 PM	#6
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	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...

11-09-2011, 01:21 PM	#7
jbrwn Member Location: Denver, CO Join Date: Mar 2011 Posts: 37	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.

11-09-2011, 11:49 AM	#2
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Could you describe what "whole genome data" means?

11-09-2011, 11:51 AM	#3
ardmore Member Location: USA Join Date: Jun 2011 Posts: 51	If we use samtools, we can select chromosome. The entire means from chr1 to chr 23.

11-09-2011, 11:57 AM	#4
swbarnes2 Senior Member Location: San Diego Join Date: May 2008 Posts: 912	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.

11-09-2011, 01:07 PM	#5
ardmore Member Location: USA Join Date: Jun 2011 Posts: 51	Can we identify the start and the end position? I just guess that start from 0 and end with a big number.