..
   (C) 2020-2022 Genozip Limited. All rights reserved.

.. _downsampling:

Downsampling and sharding
=========================

Data Types: VCF, SAM, BAM, FASTQ, FASTA, GFF3/GVF, 23andMe 

**Usage**

``genocat --downsample <rate>[,<shard>] [genozip files...]``

**Description**

Shows one line (or *read* in the case of FASTQ) in every *rate* lines. The optional *shard* parameter (0-based) determines which of the *rate* lines is shown. The default value of *shard* is 0.

Downsampling is applied as the final filter after all other filters (``--interleave``, ``--grep``, ``--regions``, ``--no-header``, ``--luft`` etc) are applied.

*Example*:

Getting the middle read of every 3 consecutive FASTQ reads (i.e. read 1 of every {0,1,2}):

::

    $ genocat my-file.fq.genozip

    @A00910:85:HYGWJDSXX:1:1101:3025:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTTGGGGGTGGGGATCCCTATCTTAGCTGTTGCAATCCCTGGGCTGCTTCAGTGTTAATAACATTCCAAA
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:8160:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NATTATGAGAGAGTGCTTTTTACAATGTTAATGACATGTTATAATAAAGTAATCTTACAATAAACAAGAA
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:9028:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NCTACAATGTGTGACAACAATAATGTAAAAGGTAGATGAAATTAAAGTACCTAGCAATATTAGGAAATTG
    +
    #FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFF:F:,FF
    @A00910:85:HYGWJDSXX:1:1101:15067:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTGTAGCATGCTCTTTGGTGCAAATTGACGAGCAGATTCTAAAAGTCACAGAGAAATGCAAAAGACCCTG
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:
    @A00910:85:HYGWJDSXX:1:1101:16007:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTTCAGAGGCTTCCGGCTAAATAGTAATACAAGTAGCACAAACAACAGAGTGAGAATGTTTATCACACTC
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:16984:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTTCTATTTTGCCCCTGAGGGTGCATCCCGAAGAGGGAAGCTATTGATTTTTAACACTAGACACATAAAC
    +
    #:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:20636:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTATATACCTATTTTCATATTTTTGTCAGTGTTGGTCAGATTTTTAGAAGTGAGATTTGCTAGCAAAAAT
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:21811:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NCTTTCAAGAGCAGCCCCAGCTCCTTAAGCTGCTGGTCCTGGTGCATCTGCTGACTTTCATGTAGAAGAT
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:1714:1016 1:N:0:CAACGAGAGC+GAATTGAGTG
    NATATTGGTCTTATGATCATAAATTTTCTCAGCATTTATATTCTGAAGAATATATATTTCCTGTTTATTT
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF

    $ genocat my-file.fq.genozip --downsample 3,1

    @A00910:85:HYGWJDSXX:1:1101:8160:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NATTATGAGAGAGTGCTTTTTACAATGTTAATGACATGTTATAATAAAGTAATCTTACAATAAACAAGAA
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:16007:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NTTCAGAGGCTTCCGGCTAAATAGTAATACAAGTAGCACAAACAACAGAGTGAGAATGTTTATCACACTC
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF
    @A00910:85:HYGWJDSXX:1:1101:21811:1000 1:N:0:CAACGAGAGC+GAATTGAGTG
    NCTTTCAAGAGCAGCCCCAGCTCCTTAAGCTGCTGGTCCTGGTGCATCTGCTGACTTTCATGTAGAAGAT
    +
    #FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

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