Triodenovo: Difference between revisions
From Genome Analysis Wiki
Jump to navigationJump to search
No edit summary |
No edit summary |
||
| Line 3: | Line 3: | ||
* 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. | ||
== 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 == | == Download == | ||
Source code of v0.04 [[Media:triodenovo.0.04.tar.gz | download]] here. Pre-compiled binary version of 0.02 [[Media:triodenovo.0.02.binary.tar.gz | download]] here. | Source code of v0.04 [[Media:triodenovo.0.04.tar.gz | download]] here. Pre-compiled binary version of 0.02 [[Media:triodenovo.0.02.binary.tar.gz | download]] here. | ||
Revision as of 23:13, 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.
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.
