Can I view output the entire genome data?

[ardmore]

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

Thanks.

[dpryan]

Could you describe what "whole genome data" means?

[ardmore]

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

[swbarnes2]

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]

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

[dpryan]

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]

to get everything just:

samtools view .bam

to get everything and the header:

samtools view -h .bam

for .sam, add the sam option

samtools view -S .sam

however, if you did want to make selections from the sam:

samtools view -S .sam chr1:0-1000000

will grab reads that meet the criteria of being on chr1 between 0 and 1000000 (inclusive)