Haplotype Inference


The phase.pl is based on HapCUT and SHAPEIT2.


Unpack the pakeage you have downloaded.

  tar -zxvf Phase.tar.gz


This will configure serveral paths for different requrements. You should replace the following paths in phase.pl with the real destination in your own system.

  my $PATH_for_extractPIRs="PATH_for_extractPIRs/extractPIRs/extractPIRs/bin";
  my $PATH_for_shapeit2="PATH_for_shapeit2";
  my $REF_panel="PATH_for_shapeit2/1000GP_Phase3";
  my $path_for_hapcut="path_for_hapcut";

Command Line


 perl phase.pl --sample sampleName --variant example.vcf --bam bamFile --gender [male|female] --reference human_genome.fa

There should be two subdirectories in your working directory: input and script. All input files should be stored in the subdirectory named input. The scripts are stored in script subdirectory.

Main Options

 Flag  Alternate  Description
--sample -s

The name of the Project. phase.pl will make a directory based on the option and the output will be stored in this fold.

--variant -v

The VCF must be sorted by chromosome and position. Besides, the VCF file should be put in the input fold.

--bam -b

The BAM file used for HapCUT. The file should be put in the input fold.

--gender -g

The gender of your sample [male|female].

--reference -r

The reference genome sequence in FASTA format.