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mattssca / vcfMAN

Pipeline for manipulating and processing of VCF files. Standardize outputs and downstream plotting for overview of relevant metrics and variant distribution.
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EXTRA: SNV ideogram #31

Closed mattssca closed 3 years ago

mattssca commented 3 years ago

Location of reference assembly gaps, benchmark regions, and diploid assembled regions to help determine why variants are not called in some regions, spread out / make all vertical, add position information (for use in manual curation/ further investigation)

mattssca commented 3 years ago

Option 1: Describe what regions are black-listed in the figure subtitle.

Option 2 (maybe add this function in the next phase?): Add black-listed regions as tracks on the ideogram in high-contrast colors.

mattssca commented 3 years ago

EDIT: waiting for black-list resources to be added to ideograms. Not as urgent, could be a part of the next phase. Also, add position information on x axis, look into flipping the plot and make the chromosomes extend vertically.

mattssca commented 3 years ago

Added