Usage
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 > plot.vl.json
To directly generate a plot in svg, png or pdf format we advice using the vega-cli and vega-lite-cli packages:
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 | vl2vg | vg2pdf > plot.pdf
To generate an interactive view within an html file use –html and capture the output to a file:
alignoth -b path/to/my.bam -r path/to/my/reference.fa -g chr1:200-300 --html > plot.html
Arguments
argument |
short |
explanation |
default |
|---|---|---|---|
bam-path |
-b |
The bam file to be visualized. |
|
reference |
-r |
The path to the reference fasta file |
|
region |
-g |
Chromosome and region for the visualization. Example: 2:132424-132924 |
|
around |
-a |
A chromosome and a base position that will define the region that will be plotted starting 500bp before and end 500bp behind the given position. Example: 2:17348 |
|
highlight |
-h |
Interval or single base position that will be highlighted in the visualization. Example: 132400-132500 or 132440 |
|
plot-all |
-p |
Plot all reads in the given region. We advise to only use this command for small bam files with a single target. |
false |
max-read-depth |
-d |
Set the maximum rows of reads that will be shown in the alignment plots |
500 |
max-width |
-w |
Set the maximum width of the resulting alignment plot |
1024 |
output |
-o |
If present, data and vega-lite specs of the generated plot will be split and written to the given directory |
|
data-format |
-f |
Sets the output format for the read, reference and highlight data |
json |
aux_tag |
-x |
Displays the given content of the aux tag in the tooltip of the plot. Multiple usage for more than one tag is possible. |
|
spec-output |
If present vega-lite specs will be written to the given file path |
||
read-data-output |
If present read data will be written to the given file path |
||
ref-data-output |
If present reference data will be written to the given file path |
||
highlight-data-output |
If present highlight data will be written to the given file path |
||
html |
If present the generated plot will inserted into a plain html file containing the plot centered which is then written to stdout |