include global LD (subsets)

#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