xenial (1) scramble.1.gz

Provided by: staden-io-lib-utils_1.14.6-2_amd64 bug

NAME

       scramble - Converts between the SAM, BAM and CRAM file formats.

SYNOPSIS

       scramble  [options] [input_file [output_file]]

DESCRIPTION

       scramble  converts  between  various  next-gen  sequencing alignment file formats, including SAM, BAM and
       CRAM. It can either act as a pipe reading stdin and writing to stdout, or on named files.

       When operating as a pipe the input type defaults to SAM or BAM, requiring the -I cram option to  indicate
       input  is  in CRAM format is appropriate. The output defaults to BAM, but can be adjusted by using the -O
       format option. When given filenames the file type is automatically chosen based on the filename suffix.

OPTIONS

       -I format
              Selects the input format, where format is one of sam, bam or cram.  Use this when  reading  via  a
              pipe  to  avoid input bytes being consumed when attempting to detect if the input is in SAM or BAM
              format.

       -O format
              Selects the output format, where format is one of sam, bam or cram.

       -1 to -9
              Sets the compression level from 1 (low compression, fast)  to  9  (high  compression,  slow)  when
              writing in BAM or CRAM format. This is only used during writing.

       -0 or -u
              Writes  uncompressed  data.  In  BAM  this  still  uses  BGZF  containers,  but  with  no internal
              compression. In CRAM it stores blocks in RAW format instead. The  option  has  no  effect  on  SAM
              output.

       -j     CRAM  encoding  only.   Add  bzip2  to  the list of compression codes potentially used during CRAM
              creation.

       -Z     CRAM encoding only.  Add lzma to the list  of  compression  codes  potentially  used  during  CRAM
              creation.   Given  the  slow  compression  speed  of  lzma, this may only be used where it gives a
              significant advantage over zlib or bzip2, but with higher compression levels (-7)  this  weighting
              is ignored as LZMA decompression speed is acceptable, albeit still slower than zlib.

       -m     CRAM  decoding  only.  Generate  MD:Z:  and  NM:I:  auxiliary  fields based on the reference-based
              compression.

       -M     CRAM encoding only.  Forcibly pack  sequences  from  multiple  references  into  the  same  slice.
              Normally  CRAM  will start a new slice when changing from one reference to another, but will still
              automatically switch to multi-reference slices if the number of sequences per  slice  becomes  too
              small.

       -R range
              Currently for CRAM input only, but SAM/BAM support is pending. This indicates a reference sequence
              name and optionally a start and end location within that reference, using the syntax  ref_name  or
              ref_name:start-end.  For efficient operation the CRAM file needs a .crai format index (built using
              the cram_index program).

       -r ref.fa
              CRAM encoding only.  Use this to specify the reference fasta file.  Note that if the input SAM  or
              BAM  file a file: or local file system based URI specified in the @SQ headers then this option may
              not be necessary.

       -s number
              CRAM encoding only.  Specifies the number of sequecnes per slice.  Defaults to 10000.

       -S number
              CRAM encoding only.   Specifies the number of slices per container.  Defaults to 1.

       -t     BAM and CRAM only.  Specifies the number  of  compression  or  decompression  threads,  adaptively
              shared between both encoding and decoding.  Defaults to 1 (no threading).

       -V version_string
              CRAM  encoding  only.   Sets  the  CRAM file format version. Supported values are "2.0", "2.1" and
              "3.0".

       -e     CRAM encoding only. Embed snippets of the reference sequence in every slice.  This means the files
              can be decoded without needing to specify the reference fasta file.

       -x     CRAM  encoding  only.   Omit  reference  based compression and instead store details of every base
              verbatim.

       -B     Experimental, encoding only.  When storing quality values, bin into 8 discrete values (plus 0), as
              typically  used by modern Illumina instruments.  (Note that the bins may not be precisely the same
              ranges.)

       -!     CRAM v3.0 and above decoding only. Do not check CRCs.   This  option  should  only  be  used  when
              attempting to recover from a data corruption.

EXAMPLES

       To convert a BAM file from stdin to CRAM on stdout, using reference MT.fa.

           some_command | scramble -I bam -O cram -r MT.fa | some_command

       The  default  CRAM output format is version 3.0, so no version needs to be specified when converting from
       2.1 to 3.0.  To perform the reverse use:

           scramble -V 2.1 in.cram out.cram

AUTHOR

       James Bonfield, Wellcome Trust Sanger Institute

                                                  March 19 2013                                      scramble(1)