Haplotype and MHL

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#!/bin/csh
#PBS -q hotel
#PBS -l nodes=1:ppn=1
#PBS -l walltime=8:00:00
#PBS -o centenarian.chr22.log
#PBS -e centenarian.chr22.err
#PBS -V
#PBS -M guoshicheng2005@gmail.com
#PBS -m abe
#PBS -A k4zhang-group
cd /home/shg047/monod/haplo/wbc
/home/shg047/monod/haplo/mergedBam2hapInfo_WGBS_25Jun15.pl /home/k4zhang/my_oasis_tscc/MONOD/All_WGBS_pooled/WGBS_pooled_mappable_bins.chr22.mld_blocks_r2-0.5.bed /home/k4zhang/my_oasis_tscc/MONOD/whole_blood_WGBS/BAMfiles/centenarian.chr22.rmdup.bam > centenarian.chr22.hapInfo.txt


cd /home/shg047/oasis/monod/haplo/
cat /home/shg047/oasis/monod/haplo/n37/*hapInfo.txt >> hapinfo.txt
cat /home/shg047/oasis/monod/haplo/wbc/*hapInfo.txt >> hapinfo.txt
cat /home/shg047/oasis/monod/haplo/hesc/*hapInfo.txt >> hapinfo.txt
cat /home/shg047/oasis/monod/haplo/tumor_wgbs/*hapInfo.txt >> hapinfo.txt
cat /home/shg047/oasis/monod/haplo/salk/*hapInfo.txt >> hapinfo.txt
cd /home/shg047/oasis/monod/haplo/
perl ~/oasis/monod/bin/haploinfo2LDR2.pl  APC chr5:111986595-112228720 < /home/shg047/oasis/monod/haplo/hapinfo.txt
perl ~/oasis/monod/bin/haploinfo2LDR2.pl  ZNF154 chr19:58206356-58222715 < /home/shg047/oasis/monod/haplo/hapinfo.txt
perl ~/oasis/monod/bin/haploinfo2LDR2.pl  SHOX2 chr3:157808200-157829413 < /home/shg047/oasis/monod/haplo/hapinfo.txt
perl ~/oasis/monod/bin/haploinfo2LDR2.pl  DIRAS3 chr1:68511645-68516481 < /home/shg047/oasis/monod/haplo/hapinfo.txt