TCGA_bed_to_meth.pbs

#PBS -S /bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l mem=10000MB
#PBS -l vmem=10000MB
#PBS -l pmem=10000MB
#PBS -l walltime=24:00:00
#PBS -q cmb
#!/bin/bash
cd "$PBS_O_WORKDIR"

sed '1d' ${IN} > ${IN}.temp # get rid of the header

grep -v -e "chrUn" -e "random" -e "hap" -e "chrX" -e "chrY" -e "chrM" ${IN}.temp > ${IN}.temp2; mv ${IN}.temp2 ${IN}.temp;

export LC_ALL=C;
awk '{print $1 "\t" $2 "\t+\tCpG\t" $7/100 "\t" $8}' ${IN}.temp | sort -k 1,1 -k 2,2g > ${IN}.meth;

rm ${IN}.temp;