Usage:
Autosomes:
./denovogear dnm auto --bcf bcf_f --ped ped_f
X chromosome in male offspring:
./denovogear dnm XS --bcf bcf_f --ped ped_f
X chromosome in female offspring:
./denovogear dnm XD --bcf bcf_f --ped ped_f
Phaser:
./denovogear phaser --dnm dnm_f --pgt pgt_f --bam bam_f --window INT[1000]
Input:
DNM:
--ped: Ped file to describe relationship between the samples.
--bcf: BCF file from samtools, contains per-sample read depths and genotype likelihoods.
Phaser:
--dnm_f: Tab delimited list of denovo mutations to be phased, format: chr pos inherited_base denovo_base.[example: 1 2000 A C]
--pgt_f: Tab delimited genotypes of child and parents at SNP sites near denovo sites, format: chr pos GT_child GT_parent1 GT_parent2.[example: 1 2000 AC AC AA]
Output:
--output_vcf: vcf file to store the output.
Parameters:
--snp_mrate: Mutation rate prior for SNPs. [1e-8]
--indel_mrate: Mutation rate prior for INDELs. [1e-9]
--pair_mrate: Mutation rate prior for paired sample analysis. [1e-9]
--indel_mu_scale: Scaling factor for indel mutation rate. [1]
--pp_cutoff: Posterior probability threshold. [0.0001]
--rd_cutoff: Read depth filter, sites where either one of the sample have read depth less than this threshold are filtered out. [10
Autosomes:
./denovogear dnm auto --bcf bcf_f --ped ped_f
X chromosome in male offspring:
./denovogear dnm XS --bcf bcf_f --ped ped_f
X chromosome in female offspring:
./denovogear dnm XD --bcf bcf_f --ped ped_f
Phaser:
./denovogear phaser --dnm dnm_f --pgt pgt_f --bam bam_f --window INT[1000]
Input:
DNM:
--ped: Ped file to describe relationship between the samples.
--bcf: BCF file from samtools, contains per-sample read depths and genotype likelihoods.
Phaser:
--dnm_f: Tab delimited list of denovo mutations to be phased, format: chr pos inherited_base denovo_base.[example: 1 2000 A C]
--pgt_f: Tab delimited genotypes of child and parents at SNP sites near denovo sites, format: chr pos GT_child GT_parent1 GT_parent2.[example: 1 2000 AC AC AA]
Output:
--output_vcf: vcf file to store the output.
Parameters:
--snp_mrate: Mutation rate prior for SNPs. [1e-8]
--indel_mrate: Mutation rate prior for INDELs. [1e-9]
--pair_mrate: Mutation rate prior for paired sample analysis. [1e-9]
--indel_mu_scale: Scaling factor for indel mutation rate. [1]
--pp_cutoff: Posterior probability threshold. [0.0001]
--rd_cutoff: Read depth filter, sites where either one of the sample have read depth less than this threshold are filtered out. [10