Pipeline Configuration

Pipeline Parameter¶

Pipeline SSCP Parameter	Tool
1. Quality Control	FastQC, Cutadapt
2. Sentieon BWA Mapping	Sentieon
3. Sentieon Sort SAM	Sentieon
4. Sentieon Mark Duplicates	Sentieon
5. Sentieon Base Recalibration	Sentieon
6. Sentieon Apply BQSR	Sentieon
7. Sentieon Coverage Metrics	Sentieon
8. Sentieon Haplotype Caller	Sentieon
9. Hard Filter VCF	Python Script
10. Pile Up	Python Script
11. Annotation Annovar	Annovar
12. Annotation VEP	Variant Effect Predictor
13. Annotation Oncotator	Python Script
14. Annotation Combination	Python Script
15. HGMD Alignement	Python Script
16. OMIM Alignment	Python Script
17. Strand Depth	Python Script
18. Region Based Annotation	Python Script
19. Customized VCF Filter	Python Script
20. Upload To OBS / Publish Output	Python Scrip

Pipeline STCP Parameter	Tool
1. Sentieon Trio Haplotype Caller	Sentieon
2. Hard Filter VCF	Python Script
3. Pile Up	Python Script
4. Annotation Annovar	Annovar
5. Annotation VEP	Variant Effect Predictor
6. Annotation Oncotator	Python Script
7. Annotation Combination	Python Script
8. HGMD Alignement	Python Script
9. OMIM Alignment	Python Script
10. Strand Depth	Python Script
11. Region Based Annotation	Python Script
12. Customized VCF Filter	Python Script
13. Upload To OBS / Publish Output	Python Script

Database	Introduction	Annotation tool
Ensembl	重要	Genome Browser Variant Effect Predictor
CCDS	由人工解读过的精华转录本	Variant Effect Predictor
Refseq	包含DNA，转录本，蛋白质	Variant Effect Predictor
gnomAD	人群频率数据库	Variant Effect Predictor
1000 Genomes Project	人群频率数据库	Variant Effect Predictor
TOPmed	人群频率数据库	Variant Effect Predictor
PrimateAI	基于基因进化保守性的评分	Variant Effect Predictor
SpliceAI	预测剪切突变	Variant Effect Predictor
CADD	人工智能打分	Variant Effect Predictor
GERP	保守型评估	Variant Effect Predictor
HGMD	致病突变数据库	Customized Tool
Clinvar	致病突变数据库	Customized Tool