concordance rate between SNP observed and SNP not observed
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6.0 years ago
nour.hadjz ▴ 20

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 • 2.9k views
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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?
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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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Okay, let's just get the program installed, first. Can you try to follow this? - https://francoismichonneau.net/2014/05/how-to-install-beagle-on-ubuntu/

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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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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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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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Sure thing!

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

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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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maybe i should install all this package separately

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You can just follow this advice, for example: https://www.digitalocean.com/community/tutorials/how-to-install-java-with-apt-get-on-ubuntu-16-04

Doing that, the most updated version of java jdk will be installed

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i followed this website: https://github.com/beagle-dev/beagle-lib/wiki/LinuxInstallInstructions and and he installed me libBeagle version 3.0 i want to install the version 4.1 of beagle beacause is the most accurate version of phasing and imputation!

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Okay, just download the JAR file from here: https://faculty.washington.edu/browning/beagle/beagle.html#download

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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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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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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)
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sorry for the way of writing my messages!! I'm working on Ubuntu when i click on th link "beagle.27Jan18.7e1.jar" found in "https://faculty.washington.edu/browning/beagle/beagle.html#introduction" i have this :

---- binary junk deleted --------

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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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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" !!

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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

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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 ?!

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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.

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ok, thank you i did it

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

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#!/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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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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Please edit your question and add this information there.

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 #!/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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