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";
Usage:
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.
| Flag | Alternate | Description |
|---|---|---|
--sample |
-s |
The name of the Project. |
--variant |
-v |
The VCF must be sorted by chromosome and position. Besides, the VCF file should be put in the |
--bam |
-b |
The BAM file used for HapCUT. The file should be put in the |
--gender |
-g |
The gender of your sample [male|female]. |
--reference
|
-r |
The reference genome sequence in FASTA format. |