WGC811.num

#!/bin/bash

#PBS -N WGC811
#PBS -q bigmem
#PBS -e WGC811_script_err
#PBS -o WGC811_script_log
#PBS -l mem=200gb,walltime=100:00:00,nodes=1:ppn=4
#HSCHED -s hschedd

#############################################################################################################################
cd /leofs/mishl_group/lim
#ref=/leofs/mishl_group/liangl/rare_dis/hg19_gatkorder

#bwa=/software/biosoft/software/bwa-0.7.10/bwa
#java=/software/biosoft/software/java1.7/jdk1.7.0_45/bin/java
#gatk=/software/biosoft/software/gatk/GenomeAnalysisTK.jar
#picard_dir=/software/biosoft/software/picard-tools-1.86
############################################################################################################################

#samtools view WGC034811U_dedup_realign_recal.bam | perl -e '$file= join "", <>;@num= $file=~m/:WGC/g;$num=@num;print "WGC_number is $num\n";' >> WGC811.num_txt 2>>WGC811.num_err
perl /leofs/mishl_group/lanyq/work/rarediease/mywork/WGC811.pl 2>WGC811.num_err
#echo -n "the total line is " >> WGC811.num_txt
#samtools view WGC034798_dedup_realign_recal.bam | wc -l >> WGC811.num_txt