scHaplotyper: Haplotype construction and visualization for genetic diagnosis using single cell DNA sequencing data

scHaplotyper performs haplotyping for genetic diagnosis using single cell DNA sequencing data. First, trio father-mother-child and father-mother-embryo “core families” are constructed, and the affected child and embryos are phased to paternal and maternal inheritance. The affected child-inherited paternal and maternal haplotypes are shown as red and yellow, respectively. Second, the haplotypes of the embryos are reconstructed by regarding the affected child as a reference. The horizontal line indicates the mutation position on the chromosome. The embryo is diagnosed as carrying paternal and/or maternal mutations when the embryo inherits the same paternal and/or maternal haplotype block as the affected child at the mutation position on the chromosome.

Platform and prerequisite

• Linux
  
• bcftools
  
• Perl SVG module is required. To test SVG installation: perldoc SVG
  

Obtain and install

Download the latest source release on github.

Unpack the file and change directory to the package directory as follows:

unzip scHaplotyper-master.zip

cd scHaplotyper-master

Configure the package:

chmod +x scHaplotyper bin/*

Data requirements

scHaplotyper requires:

• sample information file indicates identity of each sample and known disease allea carrier status of the diagnosis family.
  
• mutation information file contains mutation type and position of the gene.
  
• joint called vcf file of the family.
  

See the above example to explore the example inputs provided.

Usage and example

Usage:

./scHaplotyper SampleInfoFile MutationInfoFile VcfFile

Example:

./scHaplotyper example/Case2.SampleInfo.csv example/Case2.MutationInfo.csv example/Case2.vcf