Comments on: Identity by State SNP Analysis: Find Relatives, Test Paternity, and Determine Allele Sharing http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/ Genetics 2.0: Intelligent design and unnatural selection... Wed, 01 Feb 2012 14:55:37 +0000 hourly 1 By: admin http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/comment-page-1/#comment-722 admin Thu, 06 Jan 2011 03:38:29 +0000 http://www.chromosomechronicles.com/?p=324#comment-722 thank you for the find (updated). I have written more robust forms of the program, but none for public release. I am in the process of creating a "Genomic Playground" of sorts over the next month or so, (the lack of posts can be attributed to this). It will include a genome matching/relator application (web interface though!) thank you for the find (updated). I have written more robust forms of the program, but none for public release. I am in the process of creating a “Genomic Playground” of sorts over the next month or so, (the lack of posts can be attributed to this). It will include a genome matching/relator application (web interface though!)

]]> By: alan http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/comment-page-1/#comment-721 alan Wed, 05 Jan 2011 17:22:17 +0000 http://www.chromosomechronicles.com/?p=324#comment-721 Looks like there is a typo: "If it has less than 1% IBS-0 and greater than 5% IBS-1, then it is assumed to have 2, 1 (one allele shared). If it has less than 1% IBS-0 and greater than 5% IBS-1, then it is assumed to have 2 (both alleles shared)." Shouldn't it read "If it has less than 1% IBS-0 and than 5% IBS-1, then it is assumed to have 2 (both alleles shared)."? Would really appreciate if you have a version that allows a few of these parameters to be set and also one that allows the genome version to be specified. Thanks though for making this version available! Looks like there is a typo:

“If it has less than 1% IBS-0 and greater than 5% IBS-1, then it is assumed to have 2, 1 (one allele shared). If it has less than 1% IBS-0 and greater than 5% IBS-1, then it is assumed to have 2 (both alleles shared).”

Shouldn’t it read “If it has less than 1% IBS-0 and than 5% IBS-1, then it is assumed to have 2 (both alleles shared).”?

Would really appreciate if you have a version that allows a few of these parameters to be set and also one that allows the genome version to be specified.

Thanks though for making this version available!

]]> By: admin http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/comment-page-1/#comment-717 admin Fri, 08 Oct 2010 17:16:37 +0000 http://www.chromosomechronicles.com/?p=324#comment-717 Hello Ammar, Yes, what you are asking for is possible, and I actually write more appropriate software and license it to research institutions aimed at facilitating the type of analysis you are interested in. Please check out http://chromosoft.org to find out more. Or if you are interested, contact info@chromosoft.org. Thanks, Alex Hello Ammar,

Yes, what you are asking for is possible, and I actually write more appropriate software and license it to research institutions aimed at facilitating the type of analysis you are interested in. Please check out http://chromosoft.org to find out more. Or if you are interested, contact info@chromosoft.org.

Thanks,
Alex

]]> By: Ammar Al-Chalabi http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/comment-page-1/#comment-716 Ammar Al-Chalabi Fri, 08 Oct 2010 11:05:16 +0000 http://www.chromosomechronicles.com/?p=324#comment-716 This is an excellent tool. Is it possible to compare more than two people at a time? This would be very useful for disease linkage when there is a founder effect but no obvious pedigree. This is an excellent tool. Is it possible to compare more than two people at a time? This would be very useful for disease linkage when there is a founder effect but no obvious pedigree.

]]> By: Rick Byers http://www.chromosomechronicles.com/2009/10/22/identity-by-state-snp-analysis-find-relatives-test-paternity-and-determine-allele-sharing/comment-page-1/#comment-707 Rick Byers Sun, 23 May 2010 05:07:52 +0000 http://www.chromosomechronicles.com/?p=324#comment-707 This is cool, thanks! Any chance you're planning on sharing the source code? I've been writing my own code to analyze my SNPs, but would like to move to a common open-source Java bio framework if one exists (for leverage). BioJava doesn't seem to have any support for SNPs. Are you aware of any such framework? This is cool, thanks! Any chance you’re planning on sharing the source code? I’ve been writing my own code to analyze my SNPs, but would like to move to a common open-source Java bio framework if one exists (for leverage). BioJava doesn’t seem to have any support for SNPs. Are you aware of any such framework?

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