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- #!/usr/bin/env bash
- #PBS -N FMBY2_cnv_prep
- #PBS -j oe
- #PBS -l ncpus=8
- #PBS -l nodes=1
- #PBS -l mem=30G
- ## AZFc_u3==0
- . $script_dir/conf/conf.cfg
- cd $cnv_dir
- ls *_F_QC_plot.pdf |sed 's/_F_QC_plot.pdf//' > F.sam.list
- ls *_M_QC_plot.pdf |sed 's/_M_QC_plot.pdf//' > M.sam.list
- perl $exe_dir/com_cov_norm.pl FMBY2.exon.cov.xls
- if [ -s F.sam.list ]
- then
- nFsam=`cat F.sam.list |wc -l `
- echo $nFsam
- if [ $nFsam -lt 10 ]
- then
- cp $dat_dir/F_CNV/*.pcov .
- cat F.sam.list $dat_dir/F_CNV/F.ref.list |head -n 10 > F.ref.list
- else
- cp F.sam.list F.ref.list
- fi
- else
- rm F.sam.list
- fi
- # for male CNV REF sample list
- if [ -s M.sam.list ]
- then
- perl $exe_dir/prep_cnv_Mref.pl FMBY2.M.XY.sam.xls . M.sam.list
- grep REF $dat_dir/M_CNV/FMBY2.chr.cov.xls |cat FMBY2.M.XY.sam.xls - > FMBY2.chr.cov.xls
- nMsam=`cat FMBY2.M.XY.sam.xls |wc -l `
- if [ $nMsam -lt 16 ]
- then
- grep -v REF $dat_dir/M_CNV/FMBY2.chr.cov.xls |cat FMBY2.chr.cov.xls - |head -n 16 > FMBY2.chr.cov.xls.1
- mv FMBY2.chr.cov.xls.1 FMBY2.chr.cov.xls
- for sam in `cut -f1 FMBY2.chr.cov.xls|grep Control `
- do
- echo $sam
- cp $dat_dir/M_CNV/$sam.pcov .
- done
- fi
- test -f M.ref.list || Rscript $exe_dir/get_mby2_ref.r FMBY2.chr.cov.xls 6
- awk '$4>0.1{print $1}' FMBY2.chr.cov.xls |cat - M.ref.list |sort |uniq -c |awk '$1==2{print $2}' > M.ref.list.1
- perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov2.xls . M.ref.list.1
- Rscript $exe_dir/get_AZF_ref.r FMBY2.AZF.cov2.xls M.ref.list.2 20 && rm FMBY2.AZF.cov2.xls
- mv M.ref.list M.ref.list.cluster
- sort M.ref.list.2 |head -n 15 > M.ref.list
- else
- rm M.sam.list
- fi
- exit
- perl $exe_dir/com_cov_norm.pl FMBY2.exon.cov.xls
- perl $exe_dir/prep_cnv_Mref.pl FMBY2.chr.cov.xls
- #cat $dat_dir/FMBY2.chr.cov.xls >> FMBY2.chr.cov.xls
- test -f ref.list || Rscript $exe_dir/get_mby2_ref.r FMBY2.chr.cov.xls 6
- #grep -v 'REFDEL' ref.list > ref.list.1
- awk '$4>0.1{print $1}' FMBY2.chr.cov.xls |cat - ref.list |sort |uniq -c |awk '$1==2{print $2}' > ref.list.1
- #cp $dat_dir/FMBY2Control*.pcov .
- perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov2.xls . ref.list.1
- Rscript $exe_dir/get_AZF_ref.r FMBY2.AZF.cov2.xls ref.list.2 20 && rm FMBY2.AZF.cov2.xls
- perl $exe_dir/com_cov_norm.pl FMBY2.AZF.cov.xls . ref.list.2
- mv ref.list ref.list.cluster
- sort ref.list.2 |head -n 15 > ref.list
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