Glmvc

GLMVC: Somatic Mutation Calling Using Both DNA and RNAseq Data

Traditionally, somatic mutations are detected by examining DNA sequence. The maturity of sequencing technology has allowed researchers to screen for somatic mutations in the whole genome. Increasingly, researchers have become interested in identifying somatic mutations through RNAseq data. With this motivation, we evaluated the practicability of detecting somatic mutations from RNAseq data. Current somatic mutation calling tools were designed for DNA sequencing data. To increase performance on RNAseq data, we developed a somatic mutation caller GLMVC based on bias reduced generalized linear model for both DNA and RNA sequencing data. Through comparison with MuTect and Varscan we showed that GLMVC performed better for somatic mutation detection using exome sequencing or RNAseq data. GLMVC is freely available for download at the following website: https://github.com/shengqh/GLMVC/wiki.

Citation: Sheng Q, Zhao S, Li CI, Shyr Y, Guo Y: Practicability of detecting somatic point mutation from RNA high throughput sequencing data. Genomics 2016, 107(5):163-169.

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<a name="Changes"/> #Changes

- 2017/01/31 Version 1.3.15
 1. Bugfix: shift one base when read validation list from bed file.
- 2016/04/28 Version 1.3.14
 1. Bugfix: glm_use_raw_pvalue doesn't work.
- 2016/04/26 Version 1.3.13
 1. Enhanced: add --exclude_bed option to ignore some regions may contains a lot of false positives, for example, introduced human gene in mouse genome.
 2. Bugfix: parsing error when chromosome name contains "_".
- 2015/12/16 Version 1.3.12
 1. Enhanced: include the validation site +- 500 bases for validation mpileup to avlid the different BAQ calibration result.
 2. Bugfix: generate correct count in summary file for validation.
- 2015/12/07 Version 1.3.11
 1. Bugfix: add use_zero_minor_allele_strategy will cause filter processor exclude all candidates.
- 2015/12/07 Version 1.3.10
 1. Enhanced: add use_zero_minor_allele_strategy to pileup and filter. The candidate without minor allele detected at normal sample will be filtered by loose criteria.
- 2015/11/30 Version 1.3.9
 1. Enhanced: candidate position will not be used in mpileup for validation. Using "-l candidates.bed" option will cause different BAQ calibration result comparing to using all reads.
- 2015/11/24 Version 1.3.8
 1. Enhanced: read depth will be used as filter in call mpileup to accelerate the analysis but not in validate mpileup to report accurate result.
- 2015/11/18 Version 1.3.7
 1. Bug fix: validate: error when reading validation result without minor allele detected.
- 2015/11/17 Version 1.3.6
 1. Bug fix: remove a column distance_in_gene_range from result if gtf is provided for distance annotation
- 2015/11/16 Version 1.3.5
 1. Bug fix: table function will miss the first file if the file list doesn't have header
 2. Enhanced: table function will include refGeneAAChange in result.
- 2015/11/10 Version 1.3.4
 1. Enhanced: add option glm_use_raw_pvalue for filter
 2. New feature: summarize and build somatic mutation table
- 2015/11/05 Version 1.3.3
 1. Enhanced: add option exclude_bed to exclude specific ranges of genome in bed format
- 2015/11/01 Version 1.3.2
 1. Bug fixed: Parsing error of msm file name
- 2015/11/01 Version 1.3.1
 1. Bug fixed: Compatible with different chromosome names such like 4_JH584292_random in mm10 database