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Can I view output the entire genome data?

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  • 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.

  • #2
    Could you describe what "whole genome data" means?

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    • #3
      If we use samtools, we can select chromosome.
      The entire means from chr1 to chr 23.

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      • #4
        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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        • #5
          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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          • #6
            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...

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            • #7
              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, 02:24 PM.

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