HapICE V1.0

HapICE (Haplotype Inference for Pseudogene-mediated conversion events based on short-read next-generation sequencing data) is a solution started from the general short-read NGS BAM files and dedicated to inferring the genomic haplotypes of functional/pseudogene pairs that have highly-homologous sequences and gene conversion events frequently occurred, along with result visualization including inferred haplotype, the proportion of gene recombination events between two neighboring informative mutations, and specific reads information.

Require softwares

seqtk >= 1.3-r106

bedtools >= v2.27.1

muscle >= v3.8.31

samtools >= v1.8

blat >= v.36

R >= 3.6.0

perl >= 5

Require files

In Step1, users need to download database files under the instruction and put them under db/ directory (detailed steps check demo.sh or Step1_demo.sh). This step is not required to test Step2_demo.sh and Step3_demo.R. In Step2_demo.sh and Step3_demo.R, the test files have been prepared.

Demo

HapICE performs haplotype inference followed by three main steps: (1) prepare gene-specific reference, (2) generate reads-region mapping content matrix, and (3) functional/pseudogene haplotype inference and result visualization

Suggest users to test files under the main working directory, do not change directory to src/ or result/.

Demos script for all of the process.

demo.sh

Demos script for each of the three steps (each script could run separately).

• Part I: prepare gene-specific reference

  Step1_demo.sh

• Part II: generate reads-region mapping content matrix

  Step2_demo.sh

• Part III: functional/pseudogene haplotype inference and result visualization

  Step3_demo.R

  Rscript src/pipeline_draw.R

docker image

docker pull jargene/hapice:1.0

docker run -d -t -i docker.io/jargene/hapice:1.0 "/bin/bash"

Reference

medRxiv: https://medrxiv.org/cgi/content/short/2021.08.22.21262444v1