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Suppose I have a sam file?
Can I use samtools command to get whole genome data?
Thanks.
Can I use samtools command to get whole genome data?
Thanks.
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Could you describe what "whole genome data" means? -
If we use samtools, we can select chromosome.
The entire means from chr1 to chr 23.Comment
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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.Comment
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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.Comment
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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, 02:13 PM. Reason: I should really proof read before hitting post...Comment
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to get everything just:
to get everything and the header:Code:samtools view .bam
for .sam, add the sam optionCode:samtools view -h .bam
however, if you did want to make selections from the sam:Code:samtools view -S .sam
will grab reads that meet the criteria of being on chr1 between 0 and 1000000 (inclusive)Code:samtools view -S .sam chr1:0-1000000
Last edited by jbrwn; 11-09-2011, 02:24 PM.Comment
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