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scramble(1) Staden io_lib scramble(1) 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 read- ing stdin and writing to stdout, or on named files. When operating as a pipe the input type defaults to SAM or BAM, requir- ing the -I cram option to indicate input is in CRAM format is appropri- ate. The output defaults to BAM, but can be adjusted by using the -O format option. When given filenames the file type is automatically cho- sen 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 be- ing 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 contain- ers, 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 compres- sion speed of lzma, this may only be used where it gives a sig- nificant advantage over zlib or bzip2, but with higher compres- sion 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 ref- erences 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 num- ber 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 pro- gram). -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 op- tion 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 con- tainer. Defaults to 1. -t BAM and CRAM only. Specifies the number of compression or de- compression 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. Sup- ported 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 need- ing to specify the reference fasta file. -E CRAM encoding only. Embed snippets of the consensus sequence in every slice. This operates as per the -e option, but the con- sensus is generated from the aligned data. This does not there- fore require a reference to be known during encode (although it is still a mandatory part of the specification that the SQ SAM headers have an M5 field). It also means the files can be de- coded without needing to specify the reference fasta file. -x CRAM encoding only. Omit reference based compression and in- stead 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 Il- lumina instruments. (Note that the bins may not be precisely the same ranges.) -! CRAM v3.0 and above decoding only. Do not check CRCs. This op- tion should only be used when attempting to recover from a data corruption. -q Do not append @PG header lines with the scramble program name and arguments. -X mode Encode CRAM using a set of predefined parameters defined by mode. This are one of fast, normal / default, small or archive. fast (param: -1 -s 1000) Lightweight compression for speed and small slice size for quick fine-grained random access. normal (param: none) Default mode. This is the same as not specifying -X. For version 3.1 onwards this enables the name tokeniser ("-T"). small (param v3.0: -j -s 25000, param v3.1 or v4: -Tf -s 25000) Optimise for smaller files, with larger slices. archive (param v3.0: -j -s 100000, param v3.1 or v4: -Tfa -s 100000) Optimised for smallest files, intended for data archival. This uses a large slice size and will have poorer random access. At level 7 onwards this also enables lzma com- pression if compiled in ("-Z"). -d tag-list Discard all auxiliary tags except those listed in tag-list. The list is comma separated and contains the two letter tag codes specified as-is or with simplified regular expressions. Charac- ter classes such as "[A-W]" are permitted, but not with the negation code "^". Also "." is a synonym for any legal tag char- acter. Hence "[A-Z][A-Z0-9]" represents all tag types belonging to the official namespace. The option may be specified more than once, but it cannot be mixed with -D. -D tag-list Discard auxiliary tags listed in tag-list, keeping everything else. The list is comma separated and contains only the two letter tag codes. As with -d tag-list can be specified using a simplified regular expression. This means -D .. removes all auxiliary tags. The option may be specified more than once, but it cannot be mixed with -d. 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. The command below en- ables the experimental newer compression codecs (NB: do not use this in production) using the "small" profile, while also removing all tag types reserved for local/private use. (Also consider -d [A-Z][A-Z0-9] instead of the -D arguments.) scramble -V 3.1 -X small -D [a-zXYZ]. -D.[a-z] in.cram out.cram AUTHOR James Bonfield, Wellcome Trust Sanger Institute December 6 2022 scramble(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | EXAMPLES | AUTHOR
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