README.md

---

The pipeline is composed by using STAAR, and the scripts are midified from STAARpipeline-Tutorial.

Files Description

Preproperation

• Install xsv v0.13.0
• Download FAVORdatabase_chrsplit.csv from STAARpipeline-Tutorial
• Download FAVORannotator's Full database CSV files
  • https://favor.genohub.org
  • Check FAVORannator tab
• Untar FAVORannotator's Full database CSV files

Input file

• VCF file of a chromosome

Output file

• gds, agds, and assoc.csv

---

Execution

1. For each VCF file of a chromosome, generate a GDS generate_chr_gds.R
2. For each chromosome using the GDS generated from step 1, generate multiple csv files for variants that will be annotated Varinfo_gds.R
   • Outputs:
     • A folder <Out_Path>/chr<CHR> will be created.
     • VarInfo_chr$chr_$id.csv will be gerated in <Out_Path>/chr<CHR>
3. Annotate variants of a chromosome Annotate.R
   • Note that the script will search all csv files generated from step 2 and perform annotation
   • Outputs:
     • Anno_chr$chr_$id.csv: a CSV file containing annotated variants in VarInfo_chr$chr_$id.csv
     • Anno_chr$chr.csv: a CSV file contaning all annotated variants in all Anno_chr$chr_$id.csv
     • Anno_chr$chr_STAARpipeline.csv: a CSV file containing the variants list with annotations required for STAARpipeline of the chromosome.
4. Generate aGDS gds2agds.R using GDS and Anno_chr$chr_STAARpipeline.csv

---

Dependencies

Tools

• Biobase
• dplyr
• GENESIS
• GGally
• SeqArray
• SeqVarTools