Plink format transfer

Introduction

• input files
  --bfile --file --tfile

--bfile: read files: bed/bim/fam
--file: read ped/map

• out files
  --out

• recode

1. PED/MAP transfer to TPED/TFAM
   plink --ped test.ped --map test.map --recode --transpose --out test1
   or:
   plink --file test --recode --transpose --out test1

2. TPED/TFAM transfer to PED/MAP
   plink --tped test1.tped --tfam test1.tfam --recode --out test2
   or
   plink --tfile test1 --recode --out test2

3. PED/MAP transfer to binary file
   plink --file test --make-bed --out test3

4. TFAM/TPED transfer to binary file
   plink --tfile test1 --make-bed --out test3

5. Binary file tranfer to TPED/TFAM
   plink --bfile test3 --recode --transpose --out test4

6. Binary file transfer to PED/MAP
   plink --bfile test3 --recode --out test

• keep and remove
  --keep
  --remove

plink --bfile test --keep sample.txt --recode --make-bed --out sample

sample.txt include two colunms, first one is Family ID, second is Within-family ID

• extrac
  plink --bfile test --extract snp.txt --make-bed --out snp

Quality

• geno
• hwe
• maf
• mind

plink --bfile test --geno 0.05 --hwe 0.000001 --maf 0.5 --mind 0.1 --make-bed --out test_qc

--geno 0.05 remove one SNP if >5% missing
--mind 0.1 remove one individual if >10% missing