lines tell you programs and commands used to create the file.The Read Group line contains tags detailing the origins of the input data a chromosome), which the sequence name and length (e.g. There will be one line for every contig (e.g. lines tell you which reference sequences have been used to align the sequence again.Sorting by genomic coordinates is the most common type line tells you the version number of SAM specification and whether or not the file is sorted.The header contains information about the file, usually the following fields There are two parts to a SAM file the header and the body.
#Refid bam file format software
A SAM file is just a text file and can be read by anything a BAM file can only be accessed by using particular software e.g. BAM files are simply the binary version, which means that they are compressed and about 1/3rd the size. SAM files ( Sequence Alignment Map) contain short DNA sequences aligned to a reference genome. That document is worth reading, but I will try to simplify it further here. The SAM format specification hides the complexity well and it is easy to deceive yourself into doing the wrong thing. Further information is available on the FTP site.SAM and BAM files are considerably more complex than they first look. These lines start with # and can provide descriptions of the columns, the date the index was generated and other pieces of information, as appropriate to the file and data set. In addition, index files may have further information at the head of the file. Immediately before the body of the file there is a header line, which starts with #, that gives the column names. The index files are tab-delimited files where the data is arranged in columns. Various types of index file exist on the site, primarily listing available sequence data and alignments. Further information is available on the FTP site. Result for a column, the default value will be 0. Where data isn’t available to calculate the Provide meta information about each readgroup, with the remaining columns providing various statistics about the readgroup. The first line is a header that describes each column.
cram files, with one line per readgroup and columns separated by bas files contain statistics relating to. Current specifications for SAM/BAM, CRAM and VCF can be found at hts-specs. The specifications for these file formats continue to develop. It is able to store all variant calls from single nucleotide variants to large scale insertions and deletions. The VCF format is a tab delimited format for storing variant calls and individual genotypes. Information on working with IGSR CRAM files are available on the FTP site. The file format was designed to reduce the disk foot print of alignment data by the EBI, who provide further information on the format. This compression is driven by the reference the sequence data is aligned to. ĬRAM files are similar to BAM files but give a compressed representation of the alignment. These files and the associated SAMtools package are described in this Bioinformatics publication.Īdditional information about SAM/BAM is available at the SAMtools development site. Data file formats Alignment files: BAM and CRAM formatsīAM files are binary representations of the Sequence Alignment/Map format.