Usage

Supported formats

• BAM (indexed and sorted). A .bai file is needed.
  • Local paths and s3:// URLs are supported.
  • The index path is inferred as <bam>.bai. There is no separate CLI option for a custom index path.
  • For s3:// BAMs, place the .bai object at the inferred path and configure S3 credentials in the environment.
• VCF (.vcf and .vcf.gz) and BED (.bed and .bed.gz) files are supported as positional input files.
• Custom FASTA and 2bit reference genomes are passed with -g / --reference, not as positional track files. FASTA references require a .fai index beside the FASTA file.
• CRAM is not supported as a CLI input format. Configure CRAM tracks in a session file.

Key bindings

Quit: :q

Normal mode

Command	Notes	Example
:	Enter command mode
h/j/k/l	Move left / down / up / right
H/J/K/L	Move left / down / up / right faster
w/b	Beginning of the next / previous exon
e/ge	End of the next / previous exon
W/B	Beginning of the next / previous gene
E/gE	End of the next / previous gene
z/o	Zoom in / out
_number_ + _movement_	Move by _number_ steps	20h: left by 20 bases

Command mode

Command	Notes	Example
:q	Quit
:w	Save the active session
:wq	Save the active session and quit
:h	Help
:_pos_	Go to position on same contig	:1000
:_contig_:_pos_	Go to position on specific contig	:17:7572659
:_gene_	Go to _gene_	:KRAS
:ls / :contigs	List contigs (j/k to select, Esc, Enter)
Esc	Switch to normal mode

Filter / sort reads in command mode:

# Restore
CLEAR

# Filter by base at position 123
FILTER BASE(123)=C

Compare TGV and Vim concepts

Command	TGV	Vim	Notes
h/l	Horizontal movement	Character
w/b/e/ge	Exon	word
W/B/E/gE	Gene	WORD
j/k	Alignment track	Line
z/o	Zoom	NA	o does a different thing in Vim