"Out of South Asia": distinctive genomic profile of wild boar and domestic pig populations in South Asia

raw plink files

The ogornot file contains two groups: outgroup samples (warthog, deer pig, pygmy, and sus) and ingroup (all wild boar and domestic pigs).

Using the following command to get allele frequency of  two groups:

plink -bfile 745sample -freq -within ogornot -out frqogornot --allow-extra-chr

Using the following code to get to the number of SNPS in all ingroup samples:

awk '$3=="noog" && $6>0 && $4 ~/[ATCG]/ && $5 ~/[ATCG]/ && length($4)==1 && length($5) ==1 {print $0}'  frqogornot.frq.strat |wc -l

The result should be 104777036.