include spotlight LD

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