Documentation

Introduction

How to use PHARP

Samples in PHARP

Running time

FAQs

To facilitate studies of genetic variation and their roles in the molecular mechanism of pig complex traits, we developed the Pig Haplotypes Reference Panel (PHARP, http://alphaindex.zju.edu.cn/PHARP/index.php) database, an integrated and interactive knowledge base of pig genomes and their utilization for imputation.
In the current release, PHARP provides the following:

9,244 haplotypes (4,622 individuals, related to 140 pig breeds).
42.3 million SNPs of autosomes.
Web-based analytical tools to phase low-density genotypes (genotyped by commonly used commercial SNP arrays technology such as the Illumina PorcineSNP50 Genotyping BeadChip, the Illumina PorcineSNP60 v2 Genotyping BeadChip, and the GeneSeek GGP Porcine 80K SNP chip) and impute them into high-density genotypes.

We demonstrate its applicability for pig commercial 50K SNP arrays, by accurately imputing 2.6 billion genotypes at a concordance rate value of 0.971 in 81 Large White pigs (~17X sequencing coverage).
Overall, as a comprehensive genomic data resource with an imputation focus, PHARP provides a convenient platform for efficient phasing and imputation to facilitate genomic research of variants and their roles in pig complex traits.

Download the variants information: PHARP_v1_sites_info.gz

Download the raw data: PHARP.bam.zip

1.Sign up

Type a username and login pHARP with this later.
Make sure your email address is correct.

2.Upload your files for imputation

Parameters	Description
Job name	Please type a meaningful job name, this will help you to distinct your multiple jobs.
Ref panel	PHARP v1, contains 1006 individuals from the world-wide.
Phasing	If your VCF files have been phased, then please select the "No Phase", and they will not be phased again, which will save your time. If your VCF files need to be phased, please select "Shapeit2", then they will be phased by Shapeit2.
Mode	Choose a mode for imputation, or phase or QC for your data.
Upload file	Your VCF file is required as following: - contain only one chromosome - the chromosome name with a format as the ‘chr’ + ‘#’, such as chr1, chr2, …, chr18 - compressed by bgzip - map to SusScrofa11.1 Note: our current release does not contain sex chromosomes, chrX and chrY. Download an example of VCF file here.

3.Check processes

You can check your processes in the "job".

4.Download your results

Download your results by clicking the results link.
Meanwhile you will receive an email containing the password for unzipping your results (remember to check your email).

Abbreviations

Estimated by GGP 50K, chr6 (2,145 SNPs)

1 . Which pig assembly was used in PHARP ?

PHARP assembly is based on Sscrofa11.1.
You can download it from here.

2 . How to change chromosome names?

bcftools annotate --rename-chrs chr_name.txt chr1_18.vcf.gz | bgzip -c > chr1_18.vcf.gz

# the chr_name.txt is like this
1   chr1
2   chr2
3   chr3
4   chr4
...

3 . How to obtain a subset of VCF file for one chromosome from a VCF file containing multiple chromosomes ?

# for the vcf file
for q in {1..18}; do 
    vcftools --vcf chr1_18.vcf --chr chr$q  --recode --out chr$q
done

# for the compressed vcf file
for q in {1..18}; do 
    vcftools --gzvcf chr1_18.vcf.gz --chr chr$q --recode --out chr$q
done

# for the plink format file
for q in {1..18}; do 
    plink --bfile chr1_18 --chr chr$q --make-bed --out chr$q
done

4 . How to convert the plink to VCF format?

plink --bfile plink --recode vcf-iid --out vcf

5 . How to compress the VCF file?

bgzip your_file.vcf

6. Which parameter can be used for quality control of imputed-genotypes ?

After getting the results, you can filter it using the 'R2' paramter for quality control.

bcftools filter  -i 'R2>0.4' result.vcf.gz -Oz -o result_R2.0.4.vcf.gz

People	Email
Zhenyang Zhang	zzy2014@sjtu.edu.cn
Zhen Wang	wangzhen20@zju.edu.cn
Yuchun Pan	panyc@zju.edu.cn