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concordance rate between SNP observed and SNP not observed

Hi, i am just beginning with imputation and i try to understand the concordance rate between SNP observed and SNP not observed. can you tell me if the SNP observed are referred to reference panel ?? and what's the difference between SNP observed and not observed phasing and SNP observed and not observed not phasing ?? please if you can help me!

snp
• 5,408 views • link
updated by Biostar Biostar • written by nour.hadjz • nour.hadjz

Please provide some context... such as:

  • which program you're using?
  • where you read about these terms?
  • your end goal?
  • what data have you got?
• 1 views • link
written by Kevin Blighe Kevin Blighe

Hi, i will use Beagle sofware to impute missing data contained in a genotyping chip concerning a Malagasy population (sample) using a reference panel of 1000 genome. the imputation will concern chromosome 20. and i will repeat this operation with an european, asian and mexican population.The purpose of this study is to better understand their history, biological adaptation processes, and the prevalence of certain genetic risk factors.

i guess when i do the imputation, I need to measure the concordance rate between my imputed SNPs and the SNPs observed in the reference panel! But i don't know how to explain this part! can you bring me some HELP please?!

i want to install Beagle beagle V 4.1 on Ubuntu. If you have some advices about installation and use of Beagle I'm all ears!!

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written by nour.hadjz • nour.hadjz

just to know before trying to install Beagle, first I have to install java on Ubuntu is not it? because Beagle is implemented in java is not it ?? i will try to follow this and, I come back to you thank you for helping me Sir! I am a real beginner.

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written by nour.hadjz • nour.hadjz

Yes, but that is done via the following command:

sudo apt-get install build-essential autoconf automake \
  libtool subversion pkg-config openjdk-7-jdk

openjdk-7-jdk is a collection of JAVA libraries for run-time and development.

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written by Kevin Blighe Kevin Blighe

Ah Okay! thank you, so i will try it. And I will write to you tomorrow if you do not mind !

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written by nour.hadjz • nour.hadjz

Hi! the version of my Ubuntu is 16.04 and the site you advised me to follow is for Ubuntu 14.04, will that be fine ?? thank you.

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written by nour.hadjz • nour.hadjz

I believe it should be okay. I also use Ubuntu 16.04

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written by Kevin Blighe Kevin Blighe

I type the firt line in my terminal

sudo apt-get install build-essential autoconf automake \
  libtool subversion pkg-config openjdk-7-jdk

and the result is this:

 E: Unable to find package automake libtool
 E: Can not find package pkg-donfig 
 E: The package "openjdk-7-jdk" has no version that can be installed

is there a solution? thank you

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updated by Ram Ram • written by nour.hadjz • nour.hadjz

maybe i should install all this package separately

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written by nour.hadjz • nour.hadjz

i try to download this jar file "beagle.27Jan18.7e1.jar" ? when I click on it I have something incomprehensible. but i found some thing like that on google,is that it? Sorry for my questions!

#!/bin/bash
if [ ! -f beagle.27Jan18.7e1.jar ]; then
  echo
  echo "Downloading beagle.27Jan18.7e1.jar"
  wget http://faculty.washington.edu/browning/beagle/beagle.27Jan18.7e1.jar
fi
if [ ! -f bref.27Jan18.7e1.jar ]; then
  echo
  echo "Downloading bref.27Jan18.7e1.jar"
  wget http://faculty.washington.edu/browning/beagle/bref.27Jan18.7e1.jar
fi
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written by nour.hadjz • nour.hadjz

I'm assuming you're not conversant with java or jar files. Please Google how to execute a jar file and follow any of the Stack Overflow links.

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written by Ram Ram

Not sure why you need this fancy script...? You can just click on the link in your web browser and then the JAR file will download.

You then execute it with java -jar beagle.27Jan18.7e1.jar

Already functions for me:

java -jar beagle.27Jan18.7e1.jar 
beagle.27Jan18.7e1.jar (version 4.1)
Copyright (C) 2014-2015 Brian L. Browning
Command line syntax: java -jar beagle.27Jan18.7e1.jar [arguments]

data input/output parameters ...
  gt=<VCF file: use GT field>                        (optional)
  gl=<VCF file: use GL/PL field>                     (optional)
  gtgl=<VCF file: use GT (preferred) or GL/PL field> (optional)
  ref=<VCF file with phased genotypes>               (optional)
  out=<output file prefix>                           (required)
  excludesamples=<file with 1 sample ID per line>    (optional)
  excludemarkers=<file with 1 marker ID per line>    (optional)
  map=<PLINK map file with cM units>                 (optional)
  chrom=<[chrom] or [chrom]:[start]-[end]>           (optional)
  maxlr=<max GL/PL likelihood ratio>                 (default=5000)

general parameters ...
  nthreads=<number of threads>                       (default: machine-dependent)
  lowmem=<use low-memory algorithm (true/false)>     (default=false)
  window=<markers per window>                        (default=50000)
  overlap=<overlap between windows>                  (default=3000)
  seed=<random seed>                                 (default=-99999)

phasing and imputation parameters ...
  niterations=<number of phasing iterations>         (default=5)
  impute=<impute ungenotyped markers (true/false)>   (default=true)
  gprobs=<print GP field for imputed markers>        (default=false)
  ne=<effective population size>                     (default=1000000)
  err=<allele miscall rate>                          (default=0.0001)
  cluster=<max cM in a marker cluster>               (default=0.005)

IBD parameters ...
  ibd=<perform IBD detection (true/false)>           (default=false)
  ibdlod=<min LOD score of reported IBD segments>    (default=3.0)
  ibdcm=<min cM length of reported IBD segments>     (default=1.5)
  ibdscale=<model scale factor for Refined IBD>      (default: data-dependent)
  ibdtrim=<markers at each segment end>              (default=40)
• 0 views • link
written by Kevin Blighe Kevin Blighe

What about right-click, and then 'Save As' or 'Save Target As?

Your browser may be trying to open the JAR file as plain text

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written by Kevin Blighe Kevin Blighe

thank you i did right -click and then "save target as" on my desk and then i did on my terminal "Java -jar beagle.27Jan18.7e1.jar" but it tell me "unable to access jarfile beagle.27Jan18.7e1.jar" !!

• 0 views • link
written by nour.hadjz • nour.hadjz

Because the directory may not be in your $PATH. Make sure you cd to Desktop if you save the file there.

And then try: java -jar ./beagle.27Jan18.7e1.jar

• 0 views • link
written by GenoMax GenoMax

Hi , I had problems with my ubuntu it is blocked but finally I was able to install beagle in another computer. that's why I was absent. thanks for your previous help.

Now, how to impute on Beagle 4.1 my missing data using a referecne panel. is there a script or some commands to do this operation ?? I can not find a very precise document on that. Can you help me please ?!

• 1 views • link
written by nour.hadjz • nour.hadjz

Hello, I recommend that you open a new thread specifically about running Beagle. This thread's issue has already been solved, and it would be good to bring in other users to the discussion.

• 1 views • link
written by Kevin Blighe Kevin Blighe

Thank you. I will check again tomorrow to see if there are any responses to the new thread.

• 1 views • link
written by Kevin Blighe Kevin Blighe

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

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written by Ram Ram

Please edit your question and add this information there.

• 0 views • link
written by Ram Ram

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