Supported file formats

• bam
• bed
• bigbed
• bedpe
• bedgraph
• broadpeak
• bp (rna secondary structure)
• cram
• fasta (for reference genome sequence)
• genepred
• genepredext
• gff3
• gtf
• gwas
• interact
• maf (mutation annotation format)
• mut
• narrowpeak
• seg
• tdf
• vcf
• wig
• bigwig

Index file formats

Index files are required for bam and cram files, and strongly recommended for any text file over 2MB in size.

• bam: “bai” index files (reference samtools, igvtools)
• cram: “crai” index files
• fasta: “fai” index files (reference samtools, igvtools)
• bed, bedgraph, gff3, gtf, vcf: “.gz.tbi” tabix index files
• bed, gff3, gtf, vcf: IGV/tribble “.idx” index files.

Last updated April 2022