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.
- 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.
- Reference sequence in fasta format
- Reference sequence index file
<fasta file>.faicreated using samtools (
samtools faidx <fasta file>)
- Input BAM file
<BAM file>sorted by reference coordinates
- BAM index file
<BAM file>.baicreated using samtools (
samtools index <BAM file>)
- 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
- Execute the command line program:
java -jar cramtools-3.0.jar. Usage is printed if no arguments were given
To convert a BAM file to CRAM:
java -jar cramtools-3.0.jar cram \ --input-bam-file <bam file> \ --reference-fasta-file <reference fasta file> \ [--output-cram-file <output cram file>]
To convert a CRAM file to BAM:
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>
To build the program from source:
- To check out the source code from github you will need git client: http://git-scm.com/
- Make sure you have java 1.7 or higher: http://openjdk.java.net/ or http://www.oracle.com/us/technologies/java/index.html
- Make sure you have ant version 1.7 or higher: http://ant.apache.org/
- 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.
Reference sequence discovery
cramtools supports the following reference discovery mechanism:
- check local file provided in the command line (
- download sequences from the ENA reference registry using MD5 checksums from the SAM header
- access local cache using
REF_CACHE/REF_PATHenvironment variables. Please refer to http://www.htslib.org/doc/samtools.html for more details.
The following tools have been included into this release
- 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).
Here are some examples:
- 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.
Illimuna 8-binning scheme:
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