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

seqtk >= 1.3-r106

bedtools >= v2.27.1

muscle >= v3.8.31

samtools >= v1.8

blat >= v.36

R >= 3.6.0

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

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

Liu et.al. HapICE: Haplotype Inference for Pseudogene-mediated conversion events based on next-generation sequencing data. Submitted