include global LD (subsets)

2_reSeq-scripts/2-2_popGen/2.2.8.1.interchromLD_global_subset.sh

+#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
+