https://divingintogeneticsandgenomics.com/tags/variant-calling/ Recent content in Variant calling on Chatomics Hugo -- gohugo.io en-us © 2018 Ming 'Tommy' Tang Wed, 28 Jun 2017 14:31:00 -0700 https://divingintogeneticsandgenomics.com/archive/install-vep-for-annotating-variants/ Wed, 28 Jun 2017 14:31:00 -0700 https://divingintogeneticsandgenomics.com/archive/install-vep-for-annotating-variants/ VEP is one of the most commonly used variants annotation tools along with annovar, snpEff, but the installation and config can be very intimidating. I just went through an installation process, and put down a gist: View this gist on GitHub https://divingintogeneticsandgenomics.com/archive/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis-from/ Thu, 23 May 2013 19:57:00 -0700 https://divingintogeneticsandgenomics.com/archive/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis-from/ https://bcbio.wordpress.com/2013/05/22/scaling-variant-detection-pipelines-for-whole-genome-sequencing-analysis/?utm_source=feedlyBlue Collar Bioinformatics Scaling variant detection pipelines for whole genome sequencing analysis with 2 comments Scaling for whole genome sequencing Moving from exome to whole genome sequencing introduces a myriad of scaling and informatics challenges. In addition to the biological component of correctly identifying biological variation, it’s equally important to be able to handle the informatics complexities that come with scaling up to whole genomes. At Harvard School of Public Health, we are processing an increasing number of whole genome samples and the goal of this post is to share experiences scaling the bcbio-nextgen pipeline to handle the associated increase in file sizes and computational requirements. https://divingintogeneticsandgenomics.com/archive/what-are-phased-and-unphased-genotypes/ Mon, 20 May 2013 17:22:00 -0700 https://divingintogeneticsandgenomics.com/archive/what-are-phased-and-unphased-genotypes/ I was reading about the format of the VCF file http://www.1000genomes.org/node/101 " Genotype data are given for three samples, two of which are phased and the third unphased, with per sample genotype quality, depth and haplotype qualities (the latter only for the phased samples) given as well as the genotypes. The microsatellite calls are unphased." what do phased and unphased mean? a google search: http://www.biostars.org/p/7846/ Phased data are ordered along one chromosome and so from these data you know the haplotype. https://divingintogeneticsandgenomics.com/archive/framework-for-evaluating-variant-detection-methods-comparison-of-aligners-and/ Mon, 13 May 2013 20:11:00 -0700 https://divingintogeneticsandgenomics.com/archive/framework-for-evaluating-variant-detection-methods-comparison-of-aligners-and/ http://bcbio.wordpress.com/ Blue Collar Bioinformatics Framework for evaluating variant detection methods: comparison of aligners and callers with 5 comments Variant detection and grading overview Developing pipelines for detecting variants from high throughput sequencing data is challenging due to rapidly changing algorithms and relatively low concordance between methods. This post will discuss automated methods providing evaluation of variant calls, enabling detailed diagnosis of discordant differences between multiple calling approaches. This allows us to: