match positions to rsids

get_flipped_rsids.sh

#!/bin/bash

cd /panfs/panasas01/shared/alspac/studies/latest/alspac/genetic/variants/arrays/gwas/imputed/1000genomes/released/2015-06-25/data/quality
rm -f ~/out.txt
for i in {1..23}
do
	echo ${i}
	awk -v chr=$i '{if($1 == chr) print $2}' 1000GP_16-06-14_flipped_SNPs.txt > ~/temp
	ii=`printf %02d $i`
	zfgrep -wf ~/temp data_chr${ii}.txt.gz | awk '{ print $2 }' >> ~/out.txt

done

less ~/out.txt