include spotlight LD

include fst.local_allSpec_genome_Wide

0_data/0_resources/genes.bed

+LG09	17850000	17900000	SOX10_1
+LG12	20150000	20350000	Casz1_2
+LG12	22200000	22275000	hoxc13a
+LG17	22525000	22600000	LWS
+

2_reSeq-scripts/2-2_popGen/06_LD_spotlight/00_templates/2.2.8.1.rawLD_pair_temp.sh

+#PBS -l elapstim_req=12:00:00
+#PBS -l memsz_job=70gb
+#PBS -b 1
+#PBS -l cpunum_job=1
+#PBS -N rawLDXXnameXX
+#PBS -q clmedium
+#PBS -o 2.2.8.1.raw.LD.XXnameXX.stdout
+#PBS -e 2.2.8.1.raw.LD.XXnameXX.stderr
+
+cd $WORK/2_output/08_popGen/07_LD
+
+vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz  \
+  --keep $WORK/0_data/0_resources/vcfpops/vcftools_XXpop1XX.pop \
+  --keep $WORK/0_data/0_resources/vcfpops/vcftools_XXpop2XX.pop \
+  --bed $WORK/0_data/0_resources/genes.bed \
+  --interchrom-hap-r2 \
+  --out spotlight.XXnameXX
+
+gzip XXnameXX.interchrom.hap.ld

2_reSeq-scripts/2-2_popGen/06_LD_spotlight/00_templates/2.2.8.1.rawLD_single_temp.sh

+#PBS -l elapstim_req=12:00:00
+#PBS -l memsz_job=70gb
+#PBS -b 1
+#PBS -l cpunum_job=1
+#PBS -N rawLDXXnameXX
+#PBS -q clmedium
+#PBS -o 2.2.8.1.raw.LD.XXnameXX.stdout
+#PBS -e 2.2.8.1.raw.LD.XXnameXX.stderr
+
+cd $WORK/2_output/08_popGen/07_LD
+
+vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz  \
+  --keep $WORK/0_data/0_resources/vcfpops/vcftools_XXnameXX.pop \
+  --bed $WORK/0_data/0_resources/genes.bed \
+  --interchrom-hap-r2 \
+  --out spotlight.XXnameXX
+
+gzip XXnameXX.interchrom.hap.ld

2_reSeq-scripts/2-2_popGen/06_LD_spotlight/2.2.8.1.loop_rawLD_pairs.sh

+#!/bin/bash
+# starter script to rewrite and submit the 2.2.8.1.rawLD_pair_temp.sh script
+# once per species-pair
+
+cd $WORK/2_reSeq-scripts/2-2_popGen/06_LD_spotlight
+
+for k in nig-pue nig-uni pue-uni;do
+  POP1=$(echo $k | sed "s/-/\t/" | cut -f 1);
+  POP2=$(echo $k | sed "s/-/\t/" | cut -f 2);
+  echo -e "--- run $k ---\npop1: $POP1\npop2: $POP2"
+
+  mkdir -p $k
+
+  sed "s/XXnameXX/$k/g; s/XXpop1XX/$POP1/g; s/XXpop2XX/$POP2/g;" 00_templates/2.2.8.1.rawLD_pair_temp.sh > ./$k/2.2.8.1.rawLD.$k.sh
+
+  cd ./$k
+    qsub 2.2.8.1.rawLD.$k.sh
+  cd ..
+
+done

2_reSeq-scripts/2-2_popGen/06_LD_spotlight/2.2.8.1.loop_rawLD_single.sh

+#!/bin/bash
+# starter script to rewrite and submit the 2.2.8.1.rawLD_single_temp.sh script
+# once per species and once per location
+
+cd $WORK/2_reSeq-scripts/2-2_popGen/06_LD_spotlight
+
+for k in bel hon boc nig pue uni;do
+
+  mkdir -p $k
+
+  sed "s/XXnameXX/$k/g" 00_templates/2.2.8.1.rawLD_single_temp.sh > ./$k/2.2.8.1.rawLD.$k.sh
+
+  cd ./$k
+    qsub 2.2.8.1.rawLD.$k.sh
+  cd ..
+
+done

2_reSeq-scripts/2-2_popGen/06_LD_spotlight/2.2.8.1.rawLD_global.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
+
+vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz  \
+  --bed $WORK/0_data/0_resources/genes.bed \
+  --interchrom-hap-r2 \
+  --out spotlight.global
+
+gzip global.interchrom.hap.ld

2_reSeq-scripts/2-2_popGen/2.2.5.6.fst_local_allSpec_genome_wide.sh

+#PBS -l elapstim_req=3:00:00
+#PBS -l memsz_job=70gb
+#PBS -b 1
+#PBS -l cpunum_job=1
+#PBS -N fstLAsGw
+#PBS -q clmedium
+#PBS -o local_global_global.stdout
+#PBS -e local_global_global.stderr
+
+cd $WORK/2_output/08_popGen/05_fst
+
+vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \
+  --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigbel.pop \
+  --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_puebel.pop \
+  --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_unibel.pop \
+  --out local_allSpec_genome_wide.bel
+
+  vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \
+    --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nighon.pop \
+    --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_puehon.pop \
+    --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_unihon.pop \
+    --out local_allSpec_genome_wide.hon
+
+  vcftools --gzvcf $WORK/2_output/07_phased_variants/6_phased_mac2.vcf.gz \
+      --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_nigboc.pop \
+      --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_pueboc.pop \
+      --weir-fst-pop $WORK/0_data/0_resources/vcfpops/vcftools_uniboc.pop \
+      --out local_allSpec_genome_wide.boc
\ No newline at end of file

2_reSeq-scripts/2-2_popGen/2.2.7.gene_names.sh

@@ -18,3 +18,4 @@ for k in {01..24};
   head -n 1 HP.annotation.named.gff > subsets/HP.annotation.named.LG$k.gff;
   grep "LG"$k HP.annotation.named.gff >> subsets/HP.annotation.named.LG$k.gff;
 done
+  
\ No newline at end of file