Comments on: SNP Discovery in NGS Data, Atlas-SNP2, and VarScan http://massgenomics.org/2009/12/snp-discovery-in-ngs-data-atlas-snp2-and-varscan.html Medical genomics in the post-genome era Fri, 27 Apr 2012 18:07:26 +0000 hourly 1 http://wordpress.org/?v=3.3.1 By: Fuli Yu @ BCM-HGSC http://massgenomics.org/2009/12/snp-discovery-in-ngs-data-atlas-snp2-and-varscan.html/comment-page-1#comment-327 Fuli Yu @ BCM-HGSC Wed, 03 Feb 2010 21:09:03 +0000 http://www.massgenomics.org/?p=483#comment-327 Thank you for this blog entry on Atlas-SNP2. We have updated the URL for download with the most recent version of software and detailed documentation. Please check again. We hope that the new released version is easier to use. http://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc Thank you for this blog entry on Atlas-SNP2. We have updated the URL for download with the most recent version of software and detailed documentation. Please check again. We hope that the new released version is easier to use.

http://www.hgsc.bcm.tmc.edu/cascade-tech-software_atlas_snp-ti.hgsc

]]> By: MB http://massgenomics.org/2009/12/snp-discovery-in-ngs-data-atlas-snp2-and-varscan.html/comment-page-1#comment-298 MB Tue, 29 Dec 2009 20:47:56 +0000 http://www.massgenomics.org/?p=483#comment-298 I have not read the paper, but someone believe NQS is useful mainly because the base quality is inaccurate. When base quality is accurate, we may largely take each base independent of each other. As to the adoption of a software package, it seems to me that to publish a tool is easier than to let it adopted widely because: a) a lot more efforts are required to make the tool bug-free and user friendly; b) it is easy to make a program work well on one data set, but it is much harder to make it work well on most data sets, which is particularly true for variant callers. I have not read the paper, but someone believe NQS is useful mainly because the base quality is inaccurate. When base quality is accurate, we may largely take each base independent of each other. As to the adoption of a software package, it seems to me that to publish a tool is easier than to let it adopted widely because: a) a lot more efforts are required to make the tool bug-free and user friendly; b) it is easy to make a program work well on one data set, but it is much harder to make it work well on most data sets, which is particularly true for variant callers.

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