Difference between revisions of "Triodenovo"
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* The program '''triodenovo''' implemented a Bayesian framework for calling '''''de novo''''' mutations in '''trios''' for next-generation sequencing data. | * The program '''triodenovo''' implemented a Bayesian framework for calling '''''de novo''''' mutations in '''trios''' for next-generation sequencing data. | ||
* It takes as input a standard VCF file with PL or GL fields (storing genotype likelihoods). Commonly used callers, e.g. GATK and samtools, generate VCF files with PL values. | * It takes as input a standard VCF file with PL or GL fields (storing genotype likelihoods). Commonly used callers, e.g. GATK and samtools, generate VCF files with PL values. | ||
| + | * It calculates the likelihood of the model with de novo mutations, denoted as L1, and the likelihood of Mendelian transmission, denoted as L0, and represent the de novo evidence using DQ=-10(L1/L0) | ||
== Usage == | == Usage == | ||
Revision as of 23:39, 2 April 2014
Introduction
- The program triodenovo implemented a Bayesian framework for calling de novo mutations in trios for next-generation sequencing data.
- It takes as input a standard VCF file with PL or GL fields (storing genotype likelihoods). Commonly used callers, e.g. GATK and samtools, generate VCF files with PL values.
- It calculates the likelihood of the model with de novo mutations, denoted as L1, and the likelihood of Mendelian transmission, denoted as L0, and represent the de novo evidence using DQ=-10(L1/L0)
Usage
A command without any input will invoke triodenovo and display the following message
The following parameters are in effect:
Input files : --ped [], --in_vcf []
Output files : --out_vcf []
Denovo mutation rate : --mu [1.0e-07]
Scaled mutation rate : --theta [1.0e-03], --indel_theta [1.0e-04]
Prior of de novo ts/tv ratio : --denovo_tstv [2.00]
Non-autosome labels : --chrX [X]
Filters : --minDQ [5.00], --minTotalDepth,
--maxTotalDepth, --minDepth [5], --maxDepth,
--mixed_vcf_records
- Example 1: using default parameters
triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf
- Example 2: using --minDQ 7 to output de novo calls which are a minimum DQ of 7.
triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDQ 7
- Example 1: using --minDepth 10 to output de novo calls for which all three individuals (father, mother and child) have depth >=10.
triodenovo --ped trio.ped --in_vcf input.vcf --out denovo.vcf --minDepth 10
Input files
- A ped file, with 5 colums [see merlin documentation]. An example ped file is as follows
trio1 p1 0 0 1 trio1 p2 0 0 2 trio1 p3 p1 p2 1
- A VCF file [VCF specs]. It can contain variant information for more individuals than in the ped file.
Output fille
- The output file is specified via --out_vcf
An example use is as follows
Options
Filtering
We recommend two filtering strategies. The first is a simple filtering and the second one is more advance
Download
Source code of v0.04 download here. Pre-compiled binary version of 0.02 download here.
