Create awk_joined_vcf_fields

This script can be used to count similarities in two joined VCFs.

The VCF is easily joined with 

echo File 1 $1
echo File 2 $2
echo output $3

join -j 1 -a1 -a2 -o 0 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 1.10 1.11 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 2.10 2.11 -e missing <(grep -v "^##" $1 | awk '{if ($1=="X") $1=23;if ($1=="Y") $1=24;chrpos=($1*100000000000)+$2;print chrpos"\t"$0}' | sort -k 1,1n) <(grep -v "^##" $2 | awk '{if ($1=="X") $1=23;if ($1=="Y") $1=24;chrpos=($1*100000000000)+$2;print chrpos"\t"$0}' | sort -k 1,1n) > $3