2nd freeze of PAPGI data set

From Papgi.org

Jump to: navigation, search

Contents

List of available data set disclosed to PAPGI community


1. number of individuals : Gold dataset of fully processed genomes (done) : 100+ individuals by November 15th 2015

25 HGDP samples (10 Africans + 4 Caucasians + 4 Chinese + 3 Americans + 4 Aceanians) +
4 Central Asians + 2 Caucasian + 12 Northern Asians
11 Malaysians (2 cosmopolitans + 9 natives) + 2 Thailanders +
7 Koreans + 2 Mongolians + 5 Japanese +1 Chinese +
8 prehistoric ancient samples +
4 Indians + 3 Pakistani (including 2 Kalash) +
2 Egyptians + 2 Kuwaitis + 17 Turks

2. data files

- fastq files (available upon request)
- raw bam files (not available)
- filtered final bam files (available upon request)
- vcf files (available) : gzipped vcf format : ~ 13 GB/genome
- filtered vcf files (available)
- filtered binary vcf files (available - proprietary format smallest in size) : uncompressed binary vcf format : ~2.8GB/genome
- Approximate size of Data Files
- vcf files on the region of interest can be provided when custom bed files are provided
- Philogenetic trees from genome-wide pi values

3. Date of 2st freeze data release : from December 1st 2015

- Establishment of Service : ftp://papgi.tgi.kr
- UserID and password are available upon request. (Please, contact PAPGI bioinformatics team in UNIST by mailing to lee.kyusang.phd@gmail.com )
- Open to PAPGI consortium members only
 

4. Contribution of more genome data are welcome

- fastq files, bam files are OK
- Your contributed data are converted to standard vcf files (HG19 mapped), and then genome-wide pi value matrix (table of genome-wide pi values between individuals) can be provided.
 
* Data usage policy and guideline:
  All the PAPGI data are available to the PAPGI members only. Any publication using the PAPGI data should not precede the first official PAPGI paper. If in doubt, please contact PAPGI steering committee members (for example: Jong Bhak, jongbhak@gmail.com, Andrea Manica, am315@cam.ac.uk, Maude Phipps: maude.phipps@monash.edu, Poh San, poh_san_lai@nuhs.edu.sg, etc)
Personal tools