relatescript

#!/bin/bash

arr=($1)
IFS=$' ';
chr=${arr[0]}
ld=${arr[1]}
ud=${arr[2]}
id=${arr[3]}

id=${id/$'\r'/}
mkdir $id
cd $id
../../tabix-0.2.6/tabix -h ../../1kg/ALL.chr$chr.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz $chr:$ld-$ud | \../../vcftools/perl/vcf-subset -c ../ind.txt > test.vcf
/lustre/home/acct-bmelgn/bmelgn-3/vcftools/bin/vcftools --vcf test.vcf --recode --thin 10 --out test

../bin/RelateFileFormats \
                --mode ConvertFromVcf \
                --haps $id.haps \
                --sample $id.sample \
                -i test.recode 

../scripts/PrepareInputFiles/PrepareInputFiles.sh \
                 --haps $id.haps \
                 --sample $id.sample \
                 --ancestor ../../mask/human_ancestor_GRCh37_e59/human_ancestor_$chr.fa \
                --mask ../../mask/$chr.fasta \
                 --poplabels ../1kg.poplabels \
                 -o $id


../bin/Relate \
      --mode All \
      -m 1.25e-8 \
      -N 30000 \
      --haps $id.haps \
      --sample $id.sample \
      --map ../../recmap/$chr.rec.map \
     --seed 1 \
      -o $id
      
../scripts/EstimatePopulationSize/EstimatePopulationSize.sh \
             -i $id \
             -m 1.25e-8 \
              --poplabels ../1kg.poplabels \
              --seed 1 \
              --num_iter 3 \
              --threshold 0.5 \
              -o x$id

../scripts/DetectSelection/DetectSelection.sh \
                 -i x$id \
                 -o $id \
                -m 1.25e-8       

rm *vcf
rm x*

IFS=$'\n';

cd ..