PopulationGenomics

Workflow Steps

This workflow orchestrates a series of scripts for preprocessing, annotation, feature extraction, filtering, and summarizing variants.

Preprocessing

• scripts/preprocessing/s1_run_intjob.sh: This script runs AnnoVar/InterVar the initial job for Mount Sinai BioMe cohort II.

Annotation

• scripts/preprocessing/s2_Merge_annotation_vcf.R: This R script merges AnnoVar/InterVar annotations.

Feature Extraction

• scripts/feature_extraction/s3_Extract_PLP_PTV_variants.R: This R script extracts PLP and PTV variants on cancer genes based on ACMG/AMP guidelines.

Filtering

• scripts/filtering/s4_Filtering.PLP_s1.sh: This script filters PLP positions.
• scripts/filtering/s4_Filtering.PLP_s2.sh: This script performs additional filtering on PLP variants (ref alt).
• scripts/filtering/s5_Retain_rareSite_inVCF_filterbyAF.sh: This script retains rare sites in VCF files filtered by Alle Frequency 0.05% (0.0005).
• scripts/filtering/s6_filterExomesByVariants_PTV.sh: This script filters exomes by PTV variants.
• scripts/filtering/s7_Getting_rare_PTV.sh: This script gets rare PTV variants.

summary_df

• scripts/summary/s8_Generate_summary_df.py: This script generates a summary df for variants patients.
• scripts/summary/s9_Cal_carrier_Freq.py: This script Calculates carrier freq by Groups.