Commit 4a40cb84 authored by Kosmas Hench's avatar Kosmas Hench

include global LD (subsets)

parent 83590835
#PBS -l elapstim_req=12:00:00
#PBS -l memsz_job=70gb
#PBS -b 1
#PBS -l cpunum_job=1
#PBS -N rawLDglobal
#PBS -q clmedium
#PBS -o 2.2.8.1.raw.LD.global.stdout
#PBS -e 2.2.8.1.raw.LD.global.stderr
cd $WORK/2_output/08_popGen/07_LD
mkdir -p subsets
cd subsets
vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \
--thin 1000000 \
--interchrom-hap-r2 \
--out glob_between
for k in boc bel hon pue nig uni;do
echo $k;
pop=$WORK/0_data/0_resources/vcfpops/vcftools_$k.pop
vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \
--keep $pop \
--thin 1000000 \
--interchrom-hap-r2 \
--out glob_between.$k
done
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