haploplotR

Program for visualizing haplotype-resolved inversions, associated metrics and variant characteristics

• This set of scripts takes output produced by InvertypeR and splits data table into two data frames depending on genotype (H1 and H2)
• Haplotypes are filtered on blacklisted regions and variants intersecting centromeres
• Package outputs:
  • Clickable haplotype-resolved ideograms annotating heterozygous and homozygous variants along each chromosome
  • Genome-wide bed-files (H1 and H2) formatted for genome browser interrogation
  • Figures related to variant-size distribution
  • Variant summary metrics table
  • Haplotype speciic tables with annotations such as; probabillity scores, read counts (WW, WC, CC)

Intructions

1. Install dependencies
2. Clone/download repository
3. cd main folder
4. Put output from InvertypeR in Input folder
5. Put composite read-data browser files (BPR output) in in/bed_reads/ (wc.cw.bed.gz and ww.cc.bed.gz)
6. If session ID for UCSC genome browser is avaialble, add ID at end of line 5 in scripts/nn_haploplot.sh script, if not unique session ID will be generated
7. Execute haploplot_run.sh and follow prompted instructions

Dependencies

Package	Version	Enviroment
dplyr	0.8.5	R
gridExtra	2.3	R
ggplot2	3.3.0	R
data.table	1.12.8	R
psych	2.0.8	R
bedtools	2.26	bash
ImageMagick	7.0.10-31	bash
img2pdf	0.4.0	python
PDF-API2	1.1.14.u	perl
LBW::UserAgent	4.69	perl