Triodenovo

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.

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

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.