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  • SAMtools command line ???

    Does anyone have a quick list of the most used SAMtool command lines

    I'm really new to using UNIX:Linux and I would greatly appreciate if someone could share a pdf/doc for the SAMtool commands

    Thank you very much and hv a nice day

    Pawan

  • #2
    Running samtools without an argument will list all commands available. Then running the command without further arguments will tell you its usage.

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    • #3
      http://samtools.sourceforge.net/samtools.shtml

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      • #4
        Here's the basic workflow for most jobs. test1.sam is the output from your favorite alignment program. If not sam, you'll have to convert it SAM but many aligners are providing SAM output these days. The "export" command is a bash (bash is a common command line processor in UNIX/Linux) way of "aliasing" a longer command.

        export SAM=/usr/joeuser/samtools-0.1.8/samtools

        ${SAM} view -b -S test1.sam > test1.presort.bam

        ${SAM} sort -m 5179869184 test1.presort.bam test1

        ${SAM} index test1.bam

        ${SAM} flagstat test1.bam > test1.rpt

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        • #5
          Probably you want to start reading the FAQ. Then move to reading the manual for each
          action you want to use. Take your time for pileup.
          -drd

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          • #6
            Thank you very much guys .... I'll start with this info for now .... Have a nice evening Cheers

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            • #7
              Not related to samtools, but I believe you should read these:
              http://tldp.org/LDP/Bash-Beginners-Guide/html/
              and
              http://tldp.org/LDP/abs/html/
              You can't go much far in UNIX/Linux without knowing the shell...

              d

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