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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


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


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

  1. make it part of the base anno pipeline?