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This article is part of the supplement: The International Conference on Intelligent Biology and Medicine (ICIBM) – Genomics

Open Access Highly Accessed Research

Steps to ensure accuracy in genotype and SNP calling from Illumina sequencing data

Qi Liu12, Yan Guo1, Jiang Li1, Jirong Long3, Bing Zhang124 and Yu Shyr145*

Author Affiliations

1 Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

2 Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

3 Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, TN 37232, USA

4 Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

5 Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA

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BMC Genomics 2012, 13(Suppl 8):S8  doi:10.1186/1471-2164-13-S8-S8

Published: 17 December 2012

Additional files

Additional file 1:

Comparison of effect of different preprocessing steps. A detailed comparison of calling results with different preprocessing steps in terms of dbSNP rate, Ti/Tv ratio, novel Ti/Tv ratio and NRD for all regions, inside target regions, outside ≤ 200 bp regions, and outside > 200 bp regions from Illumina whole-exome sequencing data. Raw (blue), filterY (green), trim (black) and filterY&trim (red).

Format: PDF Size: 196KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 2:

Comparison of effect of marking duplication, realignment and recalibration. A detailed comparison of results using different steps, marking duplication, realignment and recalibration, in terms of dbSNP rate, Ti/Tv ratio, novel Ti/Tv ratio and NRD for all regions, inside target regions, outside ≤ 200 bp regions, and outside > 200 bp regions from Illumina whole-exome sequencing data. Initial alignment (black), marking duplication (yellow), realignment (violet), recalibration (blue), marking duplication followed by realignment (red), marking duplication followed by realignment and recalibration (brown).

Format: PDF Size: 285KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data

Additional file 3:

Comparison of effect of different arrangements of marking duplication, realignment and recalibration. A detailed comparison of results by arranging three steps, marking duplication, realignment and recalibration, in different orders in terms of dbSNP rate, Ti/Tv ratio, novel Ti/Tv ratio and NRD for all regions, inside target regions, outside ≤ 200 bp regions, and outside > 200 bp regions from Illumina whole-exome sequencing data. Marking duplication followed by realignment and recalibration (red), marking duplication followed by recalibration and realignment (red), realignment followed by recalibration and marking duplication (gray).

Format: PDF Size: 146KB Download file

This file can be viewed with: Adobe Acrobat Reader

Open Data