Triodenovo
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- 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
Download
Source code of v0.04 download here. Pre-compiled binary version of 0.02 download here.