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  • Help with sam flags

    Hi guys
    I would like to ask you a help with the sam format flag. I am using samtools to extract reads from a bam file. Briefly I need to extract all mapped reads in a certain range which is easy to achieve by using the samtools view command. However I need to extract together with the mapped reads also the eventual corresponding unmapped mates.
    How can I do that?
    thanks for the help!

  • #2
    There's no built-in way to do that. If the number of reads in your region of interest is relatively small, then you can "samtools view -F foo.bam region | cut -f 1 > rnames" and then just "samtools view -f 4 foo.bam | grep -f rnames > unmapped_in_region.sam". You could also write a program to do this a bit more efficiently in python (just use a dict of the read names), or just query-sort things and then have the program look for overlaps pair at a time.

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    • #3
      Thanks

      Thanks for the answer. Sam files I am using are very large so an ad hoc C or python script would not be the best option for me. I'll work on it anyway, thanks for the advice

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      • #4
        how to extract reads 1 from a sam file

        Hello, there,

        I found that samtools filter function works only for bam file. What if I have a sam file, and I would like to only keep read1 (flag: 64)?

        Do I need to convert this sam file back to bam?

        Thanks!!

        Capricy

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        • #5
          I'm pretty sure this works with sam input as well.

          samtools view -Sf 64 mapped.sam
          Last edited by Brian Bushnell; 02-27-2015, 03:18 PM. Reason: Added -S

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          • #6
            Originally posted by Brian Bushnell View Post
            I'm pretty sure this works with sam input as well.

            samtools view -f 64 mapped.sam
            Add a -S and that should work.

            Comment


            • #7
              en. My problem seems to be the missing header

              Thanks for all the replies!!

              Comment

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