Commit 83590835 authored by Kosmas Hench's avatar Kosmas Hench

include spotlight LD

include fst.local_allSpec_genome_Wide
parent 0ccac08b
LG09 17850000 17900000 SOX10_1
LG12 20150000 20350000 Casz1_2
LG12 22200000 22275000 hoxc13a
LG17 22525000 22600000 LWS
#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
#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
#!/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
#!/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
#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
#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 $WORK/0_data/0_resources/vcfpops/vcftools_uniboc.pop \
--out local_allSpec_genome_wide.boc
\ No newline at end of file
......@@ -18,3 +18,4 @@ for k in {01..24};
head -n 1 HP.annotation.named.gff > subsets/HP.annotation.named.LG$k.gff;
grep "LG"$k HP.annotation.named.gff >> subsets/HP.annotation.named.LG$k.gff;
done
\ No newline at end of file
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