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