GUI options - mjsull/HapFlow GitHub Wiki

File Menu

Create Flows

Selecting "create flow file" will open a menu that allows you to create a Flow file using a sorted BAM file and a VCF file. A location to save the Flow file must also be designated. For more details on creating a Flow File please see creating a flow file.

Change max. variants

Change the maximum number of variants shown. Flow file must be reloaded after selecting this option. Default is 2 max. variants (3 rows: 2 variants + 1 error). Variants above the max. variants value will be treated as errors. (i.e. If max. variants is set to 2 and a site has 3 alleles the third most common allele will be grouped with the errors).

Load Flows

Loads a flow file and visualizes the haplotype profile in the main window.

Tools menu

Goto Base

Go to a user selected base position in the haplotype profile.

Create Image

Create a Scalar Vector Graphics (SVG) file of the current window.

Select OTU

Select which operational taxonomic unit (OTU) to mark. This can be used to mark out a haplotype profile to separate reads.

Write OTUs

Write OTUs to BAM files. Select BAM file from which the flow file was created and a prefix for output bam files. Output files will be named prefix.1.bam for the alignments from the first OTU, prefix.2.bam for alignments from the second OTU etc.

View Menu

Hide gapped

Hides the lines that represent gaps in the reads

Show gapped

Shows the lines that represent gaps in the reads

Stretch X

Extends x-axis of the display window.

Shrink X

Shrinks the x-axis of the display window.

Stretch Y

Extends y-axis of the display window.

Shrink Y

Shrinks the y-axis of the display window.

HELP

About

Provides version details about HapFlow.

Help

Links to the HapFlow wiki.

Citing HapFlow

Citation information.

Context Menus

Right clicking on a flow will bring up a variety of options.

Details

Provides the position in the alignment of the highlighted variant, the direction and number of the reads.

Get flow readnames

Outputs the name of the reads in the selected flow as a textfile.

Write flow to BAM

Outputs the read of the selected flow as a BAM file.

Get group readnames

Outputs the name of the reads in the selected group as a textfile.

Write group to BAM

Outputs the read of the selected group as a BAM file.

Key bindings

(d) Stretch X

Extends x-axis of the display window.

(a) Shrink X

Shrinks the x-axis of the display window.

(w) Stretch Y

Extends y-axis of the display window.

(s) Shrink Y

Shrinks the y-axis of the display window.