Appendix.md

Biobank Data Analysis - Appendix

Converting Genotype Data Formats

Genotype Data Formats

There are several types of genomics data file formats. (Bold: readable format)

• Variant call format: .vcf
  • may be paired with an index file (.tbi or .csi)
• Binary variant call format: .bcf
• PLINK format: .ped and .map
• PLINK binary format: .bed, .bim, and .fam
• Oxford format: .bgen
  • may be paired with an index file (.bgi)
• Sparse allele vectors: .sav
  • may be paired with an index file (.s1r)

Softwares for Converting Genotype Data

• PLINK
• Tabix
• qctool
• bcftools
• bgenix
• and many other softwares...

Examples for Converting Genotype Data

Today's genomics data contains tens (or hundreds) of thousands of samples. Therefore, files with binary format are becoming popular. However, some data (such as KoGES genotype data) are still distributed in the form of .vcf.

VCF to PLINK binary (.bed, .bim, .fam)

If we want to convert a single .vcf file to a PLINK binary dataset, we can use the command:

plink2 \
--vcf /media/leelabsg-storage0/KBN/유전정보/KCHIP_72298/CHR1_annoINFO_filINFO0.8_72K.vcf.gz \
--make-bed \
--out /media/leelabsg-storage0/GWAS_tutorial/convert_test/CHR1_test

We can use a shell script to convert multiple files with certain patterns.

#!/bin/bash

for (( i=1; i<=22; i++ ))
do
    nohup plink2 \
        --vcf /media/leelabsg-storage0/KBN/유전정보/KCHIP_72298/CHR${i}_annoINFO_filINFO0.8_72K.vcf.gz \
        --make-bed \
        --out /media/leelabsg-storage0/GWAS_tutorial/convert_test/CHR${i}_test &
done

VCF to Oxford (.bgen)

If we want to convert our genotype data to Oxford formatted files (.bgen), we can use the command:

#!/bin/bash

for (( i=1; i<=22; i++ ))
do
    nohup plink2 \
        --vcf /media/leelabsg-storage0/KBN/유전정보/KCHIP_72298/CHR${i}_annoINFO_filINFO0.8_72K.vcf.gz dosage=DS \
        --export bgen-1.2 ref-first bits=8 \
        --out /media/leelabsg-storage0/GWAS_tutorial/convert_test/CHR${i}_test_bgen &
done

Generating Index Files

Sometimes the index file for corresponding genotype data file is missing. We can generate the index files using softwares.