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  • how to maintain headers when piping into samtools

    Hi,

    I am using bowtie2 output (which is sam format natively) to pipe into samtools as such:
    Code:
    bowtie2 <all the arguments> | samtools view -S -F 4 -b - | samtools sort - file.sorted
    but I am losing the headers when piping.

    Is there a way to maintain the headers from bowtie to samtools during the pipe. I can't seem to find an option in samtools view that does this.

    thanks

  • #2
    It works for me when I use -SbF 4 - Not sure why that is, but perhaps -F is stripping out the headers if -b output isn't stated first. You can also use reheader to fix the headers of your already generated files.

    Comment


    • #3
      use -h in samtools view. That will keep the headers.

      Comment

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