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  • Compression of Ion Torrent BAM files

    I am happy to announce that my Genozip tool now has an optimization feature specifically for Ion Torrent BAM files: --optimize-ZM optimizes the ZM field (flow signal) as follows: negative Ion Torrent flow signal values are changed to zero and positives are rounded to the nearest 10. Eg: -20,212,427 -> 0,210,430. This improves the compression significantly, as seen below.

    Example:

    > wget ftp://ftp-trace.ncbi.nih.gov/Referen...rawlib.b37.bam

    > genozip IonXpress_020_rawlib.b37.bam

    > genozip IonXpress_020_rawlib.b37.bam --optimize-ZM -o IonXpress_020_rawlib.b37.optimized.bam.genozip

    > ls -Ggh IonXpress_020_rawlib.b37*
    -rw-rw-r--+ 1 26G Aug 13 23:53 IonXpress_020_rawlib.b37.bam
    -rw-rw-r--+ 1 17G Aug 14 00:10 IonXpress_020_rawlib.b37.bam.genozip
    -rw-rw-r--+ 1 12G Aug 14 00:17 IonXpress_020_rawlib.b37.optimized.bam.genozip

    Documentation: https://genozip.com

    Paper: https://www.researchgate.net/publica...ata_Compressor
    Last edited by divon; 08-15-2021, 05:14 PM.

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