Wednesday, January 28, 2015

The Imputer

If you had done your autosomal DNA testing and you want to know the genotypes of all possible untested SNPs, this is the tool. The Imputer accurately predicts all genotypes of untested SNPs. The tool supports FTDNA, 23andMe and Ancestry autosomal build 37 files.

Usage: Select the autosomal DNA input file, enter the output filename and select an option for what to do for unidentified allele, then click 'Impute'.

Prerequisites: Microsoft .Net Framework 4.0

Screenshot:

Download : The Imputer.zip (8.31 GB)

To avoid download failures on large files from Google drive, make sure you use a download manager. Please refer to post, Downloading large files from Google Drive using Download Manager for a quick tutorial.

Source Code at GitHub

Change Log
    Version 1.0
    • Initial Release.

    Tuesday, January 27, 2015

    Assembly Converter

    Converts human genome coordinates from one assembly to another on raw autosomal DNA files. The tool supports FTDNA, Ancestry and 23andMe autosomal files. This tool replaces the obsolete build converter.

    Usage: Select the autosomal DNA input file, appropriate LiftOver chain file and enter the output filename, then click 'Convert'. The output will be in exact same format as the input, except the coordinates changed.

    Prerequisites: Microsoft .Net Framework 4.0

    Screenshot:

    Download : Assembly Converter.exe (385 Kb)

    Conversion LiftOver Chain Files
    Hg38/GRCh38 to Hg19/GRCh37hg38ToHg19.over.chain.gz (1.2 MB)
    Hg19/GRCh37 to Hg38/GRCh38hg19ToHg38.over.chain.gz (222 Kb)
    Hg19/GRCh37 to Hg18hg19ToHg18.over.chain.gz (221 Kb)
    Hg18 to Hg38/GRCh38hg18ToHg38.over.chain.gz (336 Kb)
    Hg18 to Hg19/GRCh37hg18ToHg19.over.chain.gz (137 Kb)
    The complete list of chain files for all human genome assemblies can be downloaded from here.

    Source Code at GitHub

    Change Log
      Version 1.0
      • Initial Release.

      Downloading large files from Google Drive using Download Manager

      Downloading large files are always a pain. It takes long time and worse is it if disconnects or fails just before it completes all. I rely mostly on Google Drive and sometimes upload large files. Hence, I thought it would be appropriate to post a blog explaining how to download without any issues from Google Drive using a download manager. This post assumes you are using Google Chrome and screenshots are from it. As an example, I will show how to download SNP Prophet.zip which is 13 GB, a really massive file.

      Download the file normally

      Just click on the link (or follow the link) open the link in a incognito (or make sure you haven't signed into google/gmail in that browser) and download the file normally from the browser.




      Cancel the download

      Now, cancel the download from the browser. You can cancel the download by clicking on small context menu from the download display.Once cancelled, click on 'Show all downloads' to go to downloads page.



      Copy the link

      On the downloads page, right click on the link and select 'Copy link address'


      Paste the link on Download Manager

      You can paste this copied link URL on any download manager,. Here, I had used Free Download Manager. Make sure the 'Save As' is modified as the required filename.




      Download using Download Manager

      Now, the file is being downloaded by a download manager.



      The important advantage of using a download manager is that, if any network interruption happens, the download resumes and will not download from the beginning. This helps in avoiding download failures and saving bandwidth when trying to download large files.

      Wednesday, January 21, 2015

      SNP Prophet

      If you had done your autosomal DNA testing and you want to know the genotype of an untested SNP, this is the tool. SNP prophet predicts your genotype for an untested SNP using your autosomal DNA. It has an offline version and an online version.The offline is huge but does not require any internet, nor depends on 3rd party services to be available on the internet, since everything it requires will be present in your computer. The online version however is extremely less is size but entirely depends on 3rd party APIs (OpenSNP's JSON and DAS) and their service availability. The tool supports FTDNA, Ancestry and 23andMe files.

      Usage: Select the autosomal DNA file, enter the SNP you want to know it's genotype and click 'Find GenoType'. The total process for both online and offline can take sometimes 5 to 10 minutes.

      Prerequisites: Microsoft .Net Framework 4.0

      Screenshot:

      Download :
      To avoid download failures on large files from Google drive, make sure you use a download manager. Please refer to post, Downloading large files from Google Drive using Download Manager for a quick tutorial.

      Source Code:

      Change Log
        Version 1.0
        • Initial Release.

        Tyrolean Ancient DNA

        The Tyrolean Iceman, a 5300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Oetztal Alps. The authors sequenced the complete genome of the Iceman. The authors had mentioned in the paper that they were able to extract 125,729 SNPs from all samples. I was able to convert only 2 samples ERR107308 and ERR107309 due to technical limitations.

        Download: 
        Reference:
        Keller, Andreas, et al. "New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing." Nature communications 3 (2012): 698.

        Data Used

        Monday, January 19, 2015

        GEDmatch Plus for Google Chrome


        Note: The chrome extension accesses GEDMatch website (gedmatch.com) to get details but GEDMatch neither supports nor promotes its use in any way.


        GEDmatch Plus is a chrome browser extension that adds additional functionality for GEDmatch website (www.gedmatch.com) like themes and caching.

        The extension adds a number of features to GEDmatch:

        • Several Themes, Styles etc
        • Caching of 1-to-Many, 1-to-1 Autosomal and 1-to-1 X-DNA, to reduce server load and boost performance. Caches are automatically expired after 7 days.


        Prerequisites: Google Chrome

        Screenshots:


         

         

         


        Usage: Install the addon and go to Options page and select the theme you want. Caching is enabled by default.

        Install: GEDmatch Plus Chrome Extension

        Source Code at GitHub.

        Change Log :1.0.0
        • Initial Release.

        Sunday, January 11, 2015

        Segment Compatibility

        If you want to check the segment compatibility from different kit versions from DNA testing companies, (or) if you match someone on a particular segment on lower thresholds and you want to check if that result is due to different kit versions from DNA testing companies, then this is the tool. It supports FTDNA's Affymetrix and Illumina, 23andMe's V2, V3, V4 and Ancestry files.

        Usage: To use this tool, select your kit version, your match's kit version and enter the segment details like chromosome, start and end positions. The positions should be in build 37/hg19. Then click 'Verify' button. A message box will popup to say pass/fail for the segment which is based on the requirement of atleast 100 SNPs per Mb for the specified segment. The below grid will display the available SNPs in each kit version and further below that, you find the overlapping SNP count. You can also download detailed information on the specified segment.

        Prerequisites: Microsoft .Net Framework 4.0

        Screenshot:


        Download : Segment Compatibility.exe (10.2 MB)

        Source Code at GitHub.

        Change Log
          Version 1.0
          • Initial Release.

          Thursday, January 1, 2015

          Sub Project: Autosomal Tree Visualizer

          This is a sub-project for Autosomal Pedigree Creator.

          This tool allows to visualize triangulated segments on autosomal pedigree trees. This tool is very similar to Ancient Ancestry and has all features of it, except instead of triangulated segments from ancient kits, it contains triangulated segments from the kits you select.

          Prerequisites:
          Usage:

          1. Copy the downloaded executable into Autosomal Pedigree Creator root folder. 
          2. Execute the file and it will prompt you to select the kits folder. This folder is the same folder used to generate the pedigree using Autosomal Pedigree Creator.
          3. Please wait until the kits are loaded. You can see the progress in the status bar.
          4. Once loaded, you can open entirely a different kit (a potential match) and see how segments match the kits in the pedigree.

          Screenshot:

           

          Download Autosomal Tree Visualizer.exe (686 KB)

          Source Code at GitHub.

          License: MIT License.