Detection of polymorphisms from human NGS by PED

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In this section, install of Linux(Ubuntu), setup of PED and browsing of detected polymorphisms using Platinum human sequence data provided by Illumina are described.

Following is PED analysis with ERR194146 and ERR194147 sequence data.
Project title of short reads: Whole genome sequencing and variant calls for the Coriell CEPH/UTAH 1463 family to create a "platinum" standard comprehensive set for variant calling improvement (PRJEB3381).

An example of genome view by IGV

Polymorphisms of ERR194146 are deteceted by PED with ERR194158 (Father) and ERR194159 (Mother)

Install of Ubuntu

Setup and analysis of PED

For Docker users

Visualization of detected polymorphisms using IVG

Link of PED


Akio Miyao Ph.D (
Institute of Crop Science / NARO
2-1-2, Kannondai, Tsukuba, Ibaraki, 305-8518, Japan