InvertypeR

Source code for all three components of the InvertypeR process:

1. Composite file creation
2. InvertypeR genotyping
3. Inversion visualization

Composite file creation

Dependencies:

• tool (version we use)
• samtools (1.10)
• freebayes (1.3.2)
• bcftools (1.10.2)
• R (3.5.1)
• R package GenomicRanges (1.34.0)
• R package breakpointR (1.5.1)
• R package StrandPhaseR (0.99)
• R package BSgenome.Hsapiens.UCSC.hg38 (1.4.1)

These scripts create two Strand-seq composite files, given a set of single-cell Strand-seq libraries for an individual (BAM format, indexed). Poor-quality libraries must first be removed. To create the Watson-Watson (WW or WWCC) composite file, run bash master_WWCC_composite.sh in the directory containing the single-cell BAM files. Same goes for the Watson-Crick (WC or WCCW) composite file: run bash master_WCCW_composite.sh. You must first edit the header of each master script to set user-specific variables (e.g. # threads, directory containing scripts).

InvertypeR genotyping

Dependencies:

• tool (version we use)
• R (3.5.1)
• R package invertyper (0.0.0.1)

This is done by an R package called "invertyper" that genotypes inversions in Strand-seq data. It will install a few further R packages as dependencies.

The package implements a Bayesian binomial model to genotype inversions in Strand-seq data, which must be pre-processed into two composite files (WW and WC, the latter phased). In a sense, InvertypeR can also be used to discover inversions that were not already known to be present in the data. This can be done when many putative inversions are genotyped, for example, if all inversions recorded in dbVar are genotyped with an appropriate prior. This package can also adjust the start and end coordinates of inversions in a variety of ways.

To install invertyper, run devtools::install_git(url="https://github.com/vincent-hanlon/InvertypeR", branch="main", subdir="invertyper"). You might need to install devtools first, if you don't already have it. BreakpointR doesn't always download automatically this way, though, so you may need to install it first.

For instructions on how to run the main invertyper wrapper function, load the package in R and write ?invertyper.

Inversion visualization

Dependencies:

• tool (version we use)
• R (3.5.1)
• R package dplyr (0.8.5)
• R package gridExtra (2.3)
• R package ggplot2 (3.3.0)
• R package data.table (1.12.8)
• R package psych (2.0.9)
• ImageMagick (7.0.10-0)
• python package img2pdf (0.4.0)
• perl package PDF::API2 (2.038)
• perl package LWP::UserAgent (6.49)

(Courtesy of Victor Guryev and Carl-Adam Mattsson) These scripts can be found here, along with more detailed instructions. In brief, clone the repository, install the dependencies, put an InvertypeR output file in the in/ directory, and put the two BreakpointR browserfiles for the WW and WC composite files (i.e. sample_name.WW.CC.bam_reads.bed.gz and sample_name.WC.CW.bam_reads.bed.gz from the composite file creation procedure) in the in/bed_reads/ directory. Then run bash haploplot_run.sh. A PDF ideogram linked to a UCSC Genome Browser session will be created automatically.