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.

       -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.

       -V version_string
              CRAM  encoding only.  Sets the CRAM file format version. Supported values are "1.0"
              and "2.0".

       -X     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  only.  When  encoding,  omit  reference  based  compression and instead store
              details of every base verbatim. During decoding  -x  is  still  required  to  avoid
              checking that the reference can be loaded.

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

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

       To convert from CRAM version 1.0 to CRAM version 2.0.

           scramble -V 2.0 in.cram out.cram

AUTHOR

       James Bonfield, Wellcome Trust Sanger Institute

                                          March 19 2013                               scramble(1)