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CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future.

http://www.ebi.ac.uk/ena/about/cram_toolkit

Version 3.0

• Switched to htsjdks as backend, which enables CRAM3 features.
• Please refer to http://samtools.github.io/hts-specs/CRAMv3.pdf for the CRAM file specification.
• A pre-built cramtools-3.0.jar file is included in the repository.

1. Reference sequence in fasta format <fasta file>
2. Reference sequence index file <fasta file>.fai created using samtools (samtools faidx <fasta file>)
3. Input BAM file <BAM file> sorted by reference coordinates
4. BAM index file <BAM file>.bai created using samtools (samtools index <BAM file>)
5. Download and run the program: download the prebuilt runnable jar file from https://github.com/enasequence/cramtools/blob/master/cramtools-3.0.jar?raw=true
6. Execute the command line program: java -jar cramtools-3.0.jar. Usage is printed if no arguments were given

java -jar cramtools-3.0.jar cram \
    --input-bam-file <bam file> \
    --reference-fasta-file <reference fasta file> \
    [--output-cram-file <output cram file>]

java -jar cramtools-3.0.jar bam \
    --input-cram-file <input cram file> \
    --reference-fasta-file <reference fasta file> \
    --output-bam-file <output bam file>

1. To check out the source code from github you will need git client: http://git-scm.com/
2. Make sure you have java 1.7 or higher: http://openjdk.java.net/ or http://www.oracle.com/us/technologies/java/index.html
3. Make sure you have ant version 1.7 or higher: http://ant.apache.org/
4. Run the following commands

# Clone the repository to your local directory:
git clone https://github.com/enasequence/cramtools.git

# Change to the directory: 
cd cramtools

# Build a runnable jar file: 
ant -f build/build.xml runnable

# Run cramtools
java -jar cramtools-3.0.jar 

Picard tools have been removed from cramtools because Picard supports CRAM via htsjdk.

cramtools supports the following reference discovery mechanism:

1. check local file provided in the command line (-R or --reference-fasta-file option)
2. download sequences from the ENA reference registry using MD5 checksums from the SAM header
3. access local cache using REF_CACHE/REF_PATH environment variables. Please refer to http://www.htslib.org/doc/samtools.html for more details.

• cram: (SAM/BAM to CRAM conversion)
• bam: (CRAM to SAM/BAM conversion)
• index: (CRAM indexing, can produce CRAI or BAI index)
• merge: (merges several SAM/BAM/CRAM files into one)
• fastq: (dump reads in fastq format)
• fixheader: (fix CRAM file header, namely reference sequence MD5 checksums)
• getref: (download all reference sequences mentioned in a CRAM file)
• qstat: (produce some basic quality score stats for a CRAM file)

The usage can be accessed by calling cramtools with the corresponding command as a single argument.

Bam2Cram allows to specify lossy model via a string which can be composed of one or more words separated by '-'.

Each word is read or base selector and quality score treatment, which can be binning (Illumina 8 bins) or full scale (40 values).

• N40-D8: preserve quality scores for non-matching bases with full precision, and bin quality scores for positions flanking deletions.
• m5: preserve quality scores for reads with mapping quality score lower than 5
• R40X10-N40: preserve non-matching quality scores and those matching with coverage lower than 10
• *8: bin all quality scores

• R: bases matching the reference sequence
• N: aligned bases mismatching the reference, this only applies to 'M', '=' (EQ) or 'X' BAM cigar elements.
• U: unmapped read
• Pn: pileup: capture all bases at a given position on the reference if there are at least n mismatches
• D: read positions flanking a deletion
• Mn: reads with mapping quality score higher than n
• mn: reads with mapping quality score lower than n
• I: insertions
• *: all

By default no quality scores will be preserved.

0, 1, 6, 6, 6, 6, 6, 6, 6, 6, 15, 15, 15, 15, 15, 15, 15, 15, 15,
15, 22, 22, 22, 22, 22, 27, 27, 27, 27, 27, 33, 33, 33, 33, 33, 37,
37, 37, 37, 37, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40,
40, 40, 40, 40, 40, 40 

Check for more on our web site: http://www.ebi.ac.uk/ena/about/cram_toolkit