Table 1:
Summary of the BamView standalone command line options
| Option | Parameter type | Description |
|---|---|---|
| -h | Prints the command line options. | |
| -a | File | BAM/SAM file to display. |
| -r | File | Path to the reference sequence file (FASTA, EMBL, GenBank). |
| -n | Integer | Number of bases to display in the view. |
| -c | String | Chromosome name. |
| -v | IS, S, PS, ST or C | View used on opening: IS (inferred size), S (stack, default), PS (paired stack), ST (strand), C (coverage). |
| -b | Integer | Base position to open at. |
| -o | Show the read orientation. | |
| -pc | Plot the average coverage. | |
| -ps | Plot the SNP density (only with −r). |
If no options are specified then a prompt for the BAM file is shown.