File Types

File Type	Description	Typical Extension
FASTQ	Raw reads from sequencer (often compressed)	.fastq, .fastq.gz
FASTA	Sequence data	.fasta, .fa, .fna
GTF	Gene Transfer Format (GFF2 variant)	.gtf, .gtf.gz
GFF	General Feature Format	.gff3, .gff3.gz
SAM	Sequence Alignment/Map	.sam, .sam.gz
BAM	Binary Alignment/Map	.bam
CRAM	Compressed Reference-oriented Alignment Map	.cram
VCF	Variant Call Format	.vcf,
BED	Browser Extensible Data	.bed,
TSV	Tab-Separated Values	.tsv,
CSV	Comma-Separated Values	.csv,
JSON	JavaScript Object Notation	.json,
Markdown	Markup language for documentation	.md, .markdown
TXT	Plain Text	.txt,
md5	Checksum for file integrity	.md5, .txt

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2025-05-02.