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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