scramble (1)

scramble [options] [input_file [output_file]]

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.

-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.

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

James Bonfield, Wellcome Trust Sanger Institute