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  • Samtools view -f issue

    Hi,

    I am trying to delete the unpaired reads from a BAM file. I tried with:

    $ samtools view -f1 /input_file.bam > /output_file.bam

    The resulting output is more than two times the sizes of the input, which I do not understand being the same file with less data.

    Could someone please helo me? Also alternatives way to do the same process are welcome!

    I am using samtools 0.1.18 on Terminal (Mac OSX)

  • #2
    It's producing SAM (not BAM) output. SAM is uncompressed text, BAM is compressed binary so it is smaller.
    Try the -b parameter to produce bam output.

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    • #3
      Now that was a stupid mistake i made! And I lost a morning trying to modify the most absurd parameters of the file and options of the "view"!!

      Thanks a lot Richard

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