An integrated pipeline for detection of de novo and rare inherited mutations from trios-based next-generation sequencing
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Reanalysis:

1. Input job ID:

    job ID:

Example job ID :1405150968  

2. Email

  • Email input:email Optional

3. Parameters:

De novo SNVs calling
qualitythe minimum PHRED scaled probability score, default:50
depththe minimum depth of (ref+alt) reads in either child or parents, defalt:20
QDvariant confidence from the QUAL field/unfiltered depth, defalt:8
MQ0number of reads with mapping quality equal to 0, defalt:1
PLthe maximum Phred-scaled likelihoods for genotypes in either parents or child, defalt:2
Hrunlargest contiguous homopolymer run of the variant allele in either direction on the reference, defalt:2
Flanklocation within threshold range around INDEL will be filtered, defalt:5bp
BTthat DC/DP is lower than threshold, where DC and DP represent the sequencing depth of child and parents in corresponding site,separately, defalt:0.1
PRTthe maximum percent of the covered reads (in proband) in reference calls, defalt:0.7
PARTthe minimum percent of the covered reads (in parent) in reference calls, defalt:0.95
De novo InDels calling
qualitythe minimum PHRED quality score for high-quality filtering, default:50
depththe minimum depth of (ref+alt) reads in either child or parents, defalt:20
QDvariant confidence from the QUAL field/unfiltered depth, defalt:2
MQ0number of reads with mapping quality equal to 0
PLthe maximum Phred-scaled likelihoods for genotypes in either parents or child, defalt:2
Hrunlargest contiguous homopolymer run of the variant allele in either direction on the reference, defalt:6
PRTthe maximum percent of the covered reads (in proband) in reference calls, defalt:0.7
PARTthe minimum percent of the covered reads (in parent) in reference calls, defalt:0.99
Rare inherited variants calling
qualitythe minimum PHRED quality score for high-quality filtering, default:50
depththe minimum depth of (ref+alt) reads in either child or parents, defalt:20
Database snp138 1000 genome ESP6500 CG69
FREthe maximum alternative allele frequency in selected databases, defalt:0.0001
Damaged mutation prediction
functional prediction LJB23_SIFT_pred    LJB23_Polyphen2_HDIV_pred    MutationTaster    LJB23_LRT_pred 
LJB23_MutationTaster_pred    LJB23_MutationAssessor_pred    LJB23_FATHMM_pred
LJB23_RadialSVM_pred    LJB23_LR_pred    LJB23_GERP++_predict    LJB23_PhyloP_predict   
LJB23_SiPhy_predict   
damage predictionnumber of softwares to define the locus as damaged, default:8
Non-coding region analysis
non-coding Whether analysing the variants located in non-coding region, default:yes


Copyright©2014, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.