Annopipe

Annotation

Step	Single/Trio	Trio	Dependencies	Notes
Slice by genepanel	bedtools slice		transcripts	Handled by anno
Filtus prep		annotation_prep_filtus	transcripts, capturekit	Run before annotation?
Filtus analysis		annotation_filtus_analysis	pedigree	Run before annotation?
Filtus to VCF		annotation_filtus_to_vcf		Run before annotation?
Annotation	vt/vep/vcfanno		Not relevant	Handled by anno
Filter with frequency report		vcf_filter_on_freq_report	capturekit

CNV Calling and Annotation

Only run if cnv file exists in preprocessed

Step	Single/Trio	Trio	Dependencies	Notes
CNV: filter by genepanel	bedtools intersect		transcripts
CNV: annotate	cnvScan_annotate		params_resources, params_cnv_db	Need to move cnvdata to anno1

QC

Step	Single/Trio	Trio	Dependencies	Notes
QC		gatk T SelectVariants	fasta
Coverage calculation	qc_coverage		slop2
	qc_analysis		capturekit, noslop_list and contamination_test, transcripts
Coverage report	report_coverage_single		report_config
Report warning	report_warning		captureKit

QC join

Step	Single/Trio	Trio	Dependencies	Notes
Coverage report		report_coverage_trio	pedigree, coveragetranscriptproband/mother/father, transcripts, report_config

Excel report

Step	Single	Trio	Dependencies	Notes
Excel report		report_trio	pedigree, transcripts
Excel report	report_single		capturekit, transcripts

Ella

Step	Single/Trio	Trio	Dependencies	Notes
ella export	bedtools intersect		transcripts, ella_remove

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1. make it part of the base anno pipeline? ↩