Changes
From Statistical Genetics Courses
==RV-TDT exercise==
vtools init rvtdt
vtools import --format vcf data/data.vcf --build hg19
vtools select func_variant -o chr pos refGene.name2 maf --header > vat_export.anno
# Mendelian error and recode
plink --noweb --tfile vat_export --recode12 --me 1 1 --set-me-missing --make-bed --out "noME" plink --bfile noME --recode12 --out "recode12_noME"
sort -n -k1 -k6 -k2 recode12_noME.ped | sed 's/ /\t/g' | cut -f1,3,4,5 --complement > linkage.ped
cut -f2 recode12_noME.map | awk 'BEGIN{OFS="\t";} {print "M",$0}' | sed '1i\I\tid\nA\tDisease' > linkage.dat
