Binary SAM format. BAM files are binary formatted, indexed and allow random access.


Binary VCF.


Browser Extensible Data format. A text file format used to store genomic regions as coordinates and associated notations.


Utility in the htslib package to block compress genomic data files.


Stands for Compact Idiosyncratic Gapped Alignment Report and represents a compressed (run-length encoded) pairwise alignment format. It was first defined by the Exonerate Aligner, but was alter adapted and adopted as part of the SAM standard and many other aligners. In the Python API, the cigar alignment is presented as a list of tuples (operation,length). For example, the tuple [ (0,3), (1,5), (0,2) ] refers to an alignment with 3 matches, 5 insertions and another 2 matches.

The portion of reads aligned to a single base in the

reference sequence.


The sequence that a tid refers to. For example chr1, contig123.


CRAM is a binary format representing the same sequence alignment information as SAM and BAM, but offering significantly better lossless compression than BAM.


Utility in the samtools package to index fasta formatted files.


Simple text format containing sequence data, with only the bare minimum of metadata. Typically used for reference sequence data.


Simple text format containing sequence data and associated base qualities.


Retrieving all mapped reads mapped to a region.

An individual’s collection of genes. It can also refer to the two alleles

inherited for a particular gene.

The Gene Transfer Format is a file format used to hold information

about gene structure.

hard clipping
hard clipped

In hard clipped reads, part of the sequence has been removed prior to alignment. That only a subsequence is aligend might be recorded in the cigar alignment, but the removed sequence will not be part of the alignment record, in contrast to soft clipped reads.




Synonym for contig.


A genomic region, stated relative to a reference sequence. A region consists of reference name (‘chr1’), start (15000), and end (20000). Start and end can be omitted for regions spanning a whole chromosome. If end is missing, the region will span from start to the end of the chromosome. Within pysam, coordinates are 0-based half-open intervals, i.e., the first base of the reference sequence is numbered zero; and the base at position start is part of the interval, but the base at end is not.

When a region is written as a single string using samtools-compatible notation, e.g., ‘chr1:15001-20000’, the string’s coordinates instead represent a 1-based closed interval, i.e., both (1-based) positions 15,001 and 20,000 are part of the interval. (This example denotes the same 5,000-base region as the example in the previous paragraph.)


A textual format for storing genomic alignment information.

sam file

A file containing aligned reads. The sam file can either be a BAM file or a TAM file.

soft clipping
soft clipped

In alignments with soft clipping part of the query sequence are not aligned. The unaligned query sequence is still part of the alignment record. This is in difference to hard clipped reads.


Utility in the htslib package to index bgzip compressed files.

tabix file

A sorted, compressed and indexed tab-separated file created by the command line tool tabix or the commands tabix_compress() and tabix_index(). The file is indexed by chromosomal coordinates.

tabix row

A row in a tabix file. Fields within a row are tab-separated.


Text SAM file. TAM files are human readable files of tab-separated fields. TAM files do not allow random access.


The sequence that a read has been aligned to. Target sequences have bot a numerical identifier (tid) and an alphanumeric name (Reference).


The target id. The target id is 0 or a positive integer mapping to entries within the sequence dictionary in the header section of a TAM file or BAM file.


Variant Call Format.