Tag Archives: 23andme - Page 3

23andme Conversion to PED

Posted by on February 4, 2011 13 comments

Someone asked about how to convert a 23andme raw data file to the Plink format. I threw together a very simple Unix script to do that and I am sharing it here:

#!/bin/bash
if test -z "$1"
then
	echo "23andme raw data filename not supplied as argument."
	exit 0
fi
echo "Family ID: "
read fid
echo "Individual ID: "
read id
echo "Paternal ID: "
read pid
echo "Maternal ID: "
read mid
echo "Sex (m/f/u): "
read sexchr
if [[ $sexchr == m* ]]
then
	sex=1
elif [[ $sexchr == f* ]]
then
	sex=2
else
	sex=0
fi
pheno=0
echo "$fid $id $pid $mid $sex $pheno" > $id.tfam
dos2unix $1
sed '/^\#/d' $1 > $id.nocomment
awk '{ if (length($4)==1) print $2,$1,"0",$3,substr($4,1,1),substr($4,1,1); else
    print $2,$1,"0",$3,substr($4,1,1),substr($4,2,1) }' $id.nocomment > $id.tped
plink --tfile $id --out $id --make-bed --missing-genotype - --output-missing-genotype 0

Well that's it! You can easily create a Perl script to do the same but this was faster for me.

This script creates three files: *.bed, *.bim and *.fam, which are the binary format files for Plink. You can then use Plink to merge multiple files, filter SNPs or individuals and do other processing.

UPDATE: A Perl script to do the same:

#!/usr/bin/perl -w
 
$numArgs = $#ARGV + 1;
if ($numArgs < 1) {
        print "23andme raw data filename not provided.\n";
        exit 0;
}
 
$file = $ARGV[0];
 
print "Family ID: ";
$fid = <STDIN>;
chomp $fid;
print "Individual ID: ";
$id = <STDIN>;
chomp $id;
print "Paternal ID: ";
$pid = <STDIN>;
chomp $pid;
print "Maternal ID: ";
$mid = <STDIN>;
chomp $mid;
print "Sex (m/f/u): ";
$sexchr = <STDIN>;
if (lc(substr($sexchr,0,1)) eq "m") {
        $sex = 1; }
elsif (lc(substr($sexchr,0,1)) eq "f") {
        $sex = 2; }
else {
        $sex = 0; }
$pheno = 0;
$tfamname = ">" . $id . ".tfam";
open(TFAM, $tfamname);
print TFAM "$fid $id $pid $mid $sex $pheno";
close TFAM;
 
open(INFILE,$file);
open(TPED,">" . $id . ".tped");
while (<INFILE>) {
        next if /#.*/;
        chomp;
        my($rsid,$chr,$pos,$geno) = split(/\s/);
        if (length($geno)==1) {
                $geno1 = $geno;
                $geno2 = $geno;
        }
        else {
                $geno1 = substr($geno,0,1);
                $geno2 = substr($geno,1,1);
        }
        print TPED "$chr $rsid 0 $pos $geno1 $geno2\n";
}
close TPED;
close INFILE;

That should work on Linux, Microsoft Windows and Mac OS X.

Participation Update

Posted by on January 31, 2011 8 comments

I have a total of 23 participants in the project right now who have sent me their raw data. The following groups are represented:

  • Punjab: 7
  • Tamil: 4
  • Iran: 3
  • Bengal: 2
  • Andhra Pradesh: 2
  • Bihar: 1
  • Anglo-Indian: 1
  • Roma: 1
  • Karnataka: 1
  • Kashmir: 1

There is still a lot of ethnicities and regions missing. Uttar Pradesh comes to mind as the biggest one.

23andme v3 Data

Posted by on January 25, 2011 1 comment

The results from 23andme's new version 3 chip started coming in yesterday and I have already got three samples of the new chip.

I counted 966,977 SNPs on the new chip. It seems to have about 547,000 SNPs in common with version 2 (which had about 578,000). Also, the version 3 data has about 230,000 SNPs in common with my reference dataset (out of a total of 241,000). Which is a long way of saying that the v3 data is very usable for my project.

Therefore, if you are from South Asia or neighboring countries and got your spanking new results, please participate and send your data over.

Participants So Far

Posted by on January 24, 2011 11 comments

While I am analyzing the data, checking for errors and making sure the results I am getting are valid, here is some information about participants till now.

So far I have got 11 participants send me their raw data. Of these eleven, ten have some South Asian ancestry.

The regions/ethnicities they cover are:

  • Punjab
  • Bengal
  • Bihar
  • Tamil Nadu
  • Telegu
  • Anglo-Indian

Of these, Punjabis are the only ones I have multiple samples of. So I definitely need more samples of the other ethnicities. And there are lots of ethnicities/regions I haven't gotten any participants in.

It would be great for this project if we got a few participants from each state/province of India and Pakistan. So if you know someone who is from our target regions and has tested with 23andme, please spread the word.

If you tested with 23andme during their Christmas sale, I am hearing that results are going to start coming in starting today.

Introduction

Posted by on January 19, 2011 5 comments

I have become interested (some would say obsessed) with genetics recently. I wrote about getting my DNA test done and there's a lot more about my own results that I plan to bore you with.

One fun application of genetic testing is inferring ancestry: Which ancestral group are you descended from? Can we estimate the admixture of the different population groups you are descended from?

Most DNA testing companies provide information about ancestry and genetic genealogy has taken off. With several genome databases (HapMap, HGDP, etc) and software (like plink, admixture, Structure) publicly available, the days of the genome bloggers are here. And I am trying to be the latest one.

In starting this project, I have been inspired by the Dodecad Ancestry Project by Dienekes Pontikos and Eurogenes Ancestry Project by David Wesolowski. The catalyst for this project was my friend Razib who I bug whenever I need to talk genetics.

What is Harappa Ancestry Project?
It is a project to analyze (autosomal) genetic data of participants of South Asian origin for the purpose of providing detailed ancestry information. So the focus of the project is on South Asians: Indians, Pakistanis, Bangladeshis and Sri Lankans.

The project will collect 23andme raw genetic data from participants to better understand the ancestry relationships of different South Asian ethnicities.

I have named it after Harappa, an archaeological site of the Indus Valley Civilization in Punjab, Pakistan.

Participation
People of South Asian origin, or from neighboring countries, are eligible to participate. The list of countries of origin I am accepting are as follows:

  • Afghanistan
  • Bangladesh
  • Bhutan
  • Burma
  • India
  • Iran
  • Maldives
  • Nepal
  • Pakistan
  • Sri Lanka
  • Tibet

Right now, I am only accepting raw data samples from people who have tested with 23andme.

Please do not send samples from close relatives. I define close relatives as 2nd cousins or closer. If you have data from yourself and your parents, it might be better to send the samples from your parents (assuming they are not related to each other) and not send your own sample.

If you are unsure if you are eligible to participate, please send me an email (harappa@zackvision.com) to inquire about it before sending off your raw data.

What to send?
Please send your All DNA raw data text file (zipped is better) downloaded from 23andme to harappa@zackvision.com along with ancestral background information about you and all four of your grandparents. Background information would include where they were born, mother tongue, caste/community to which they belonged, etc. Please provide as much ancestry information as possible and try to be specific. Do especially include information about any ancestry from outside South Asia.

Data Privacy
The raw genetic data and ancestry information that you send me will not be shared with anyone.

Your data will be used only for ancestry analysis. No analysis of physical or health/medical traits will be performed.

The individual ancestry analysis published on this blog will be done using an ID of the form HRPnnnn known to only you and me.

What do you get?
All results of ancestry analysis (individual and group) will be posted on this blog under the Harappa Ancestry Project category. This will include admixture analysis as well as clustering into population groups etc.

I suggest you read about Dienekes' analysis on South Asians for an idea about what to expect.

You can access all blog posts related to this project from the Harappa Ancestry Project link on the navigation menu on every page of my website. You can also subscribe to the project feed.