-
Notifications
You must be signed in to change notification settings - Fork 2
GUI options
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 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).
Loads a flow file and visualizes the haplotype profile in the main window.
Go to a user selected base position in the haplotype profile.
Create a Scalar Vector Graphics (SVG) file of the current window.
Select which operational taxonomic unit (OTU) to mark. This can be used to mark out a haplotype profile to separate reads.
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.
Hides the lines that represent gaps in the reads
Shows the lines that represent gaps in the reads
Extends x-axis of the display window.
Shrinks the x-axis of the display window.
Extends y-axis of the display window.
Shrinks the y-axis of the display window.
Provides version details about HapFlow.
Links to the HapFlow wiki.
Citation information.
Right clicking on a flow will bring up a variety of options.
Provides the position in the alignment of the highlighted variant, the direction and number of the reads.
Outputs the name of the reads in the selected flow as a textfile.
Outputs the read of the selected flow as a BAM file.
Outputs the name of the reads in the selected group as a textfile.
Outputs the read of the selected group as a BAM file.
Extends x-axis of the display window.
Shrinks the x-axis of the display window.
Extends y-axis of the display window.
Shrinks the y-axis of the display window.