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Overview of different data formats

Overview of fasta, fastq, BED, SAM/BAM, VCF files, the filetypes used in a typical next generation sequencing (NGS) pipeline
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Sequencing data can be saved in specific formats to make it easier to collect, store, analyse, and disseminate information. Each format will specify the manner in which each level of the genetic analysis is employed as it encodes the obtained information from each step of the pipeline, going from the sequencer data output, the alignment and all the way to the variant calling. The majority of data formats are text-based and can be explored using a simple text editor (apart from FAST5, which is specific to Oxford Nanopore Technologies and BCL files used in Illumina pipelines). Several technologies are attached to their own data formats, but there are several that are widely used in NGS data analysis. The data format flow in a typical NGS data analysis pipeline is generally composed of: FASTQ, BAM/SAM and VCF.


The format for sequencing data files known as FASTQ is based on text and may hold both raw sequence data as well as quality scores. A FASTQ file normally uses four lines per sequence: the first line begins with a ‘@’ character, the sequence identifier and an optional description; the second line has the raw sequence in letters; the third line, begins with a ‘+’ and has the same sequence ID and any description; and line 4 encodes the quality values for the sequence in line two.


After alignment, the file format that holds information on how our target sequence aligns to a reference is called SAM, which stands for Sequence Alignment/Map format. A BAM file is a binary compressed version of the SAM format, thus we refer to both formats as SAM/BAM. It is a TAB-delimited text format with an optional header section and an alignment section. Header lines begin with an ‘@,’ whereas alignment lines do not. Each tab acts as a separator between columns. A SAM file has 11 mandatory columns that hold information on each alignment, they hold information as follows: 1. Query template NAME, 2. bitwise FLAG, 3. Reference sequence NAME, 4. 1-based leftmost mapping POSition, 5. MAPping Quality, 6. CIGAR string, 7. Reference name of the mate/next read, 8. Position of the mate/next read, 9. observed Template LENgth, 10. segment SEQuence and 11. ASCII of Phred-scaled base QUALity+33. The optional fields must follow TAG:TYPE:VALUE, for them to be explicit and the information accessible for further analysis. After alignment comes variant calling.


The file format that holds variant calls information is called the variant call format or VCF. A single VCF file can hold many millions of variants. A VCF format is also a text-based, tab-delimited file. It contains meta-information lines that start with the characters ‘##’, a header that starts with only one ‘#’ and then data lines each containing information about a position in the genome. The format also has the ability to contain genotype information on samples for each position. It consists of 8 mandatory columns named in the header. These columns are as follows: 1. #CHROM: chromosome number, 2. POS: position, 3. ID: identifier of the variant, 4. REF: the reference allele, 5. ALT: the alternative allele, 6. QUAL: Phred-scaled quality score, 7. FILTER: filter status and, 8. INFO: additional information. The VCF can have more rows and columns, depending on how many samples are being analysed. One column is added for each sample, and one row is added for each variant or genotype that is found.

Relational diagram showing the links between file formats described in the preceding article text. It will not be examined for this course and is used here decoratively.

Click here to enlarge the image

Figure 1 – Diagram of the sequencing process and analyses. Source: Bioinformatics at COMAV


Sequence Alignment/Map Format Specification

The Variant Call Format (VCF)

Bioinformatics at COMAV

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