#PBS -N test
#PBS -j oe
#PBS -l ncpus=4
#PBS -l nodes=1
#PBS -l mem=20G
#cd ${PBS_O_WORKDIR}
bed=$1
home=/home/guochangquan
gatk=/cgdata/guocq/soft/GATK/4.1.2.0/gatk
verify=/cgdata/guocq/soft/verifyBamID_1.1.3/verifyBamID/bin/verifyBamID
b37=$home/database/GATK/b37/human_g1k_v37_decoy.fasta
b37_dict=$home/database/GATK/b37/human_g1k_v37_decoy.dict
idtwes_b37=/cgdata/guocq/script/wes-cnv/xgen-exome-research-panel-probes-b37.bed
mby2_b37=/cgdata/guocq/script/MBY2-b37/MBY2_20180802.b37.6.bed
bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.vcf.gz
idtwes_bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.IDTWES.vcf.gz
mby2_bia_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.MBY2.ip80.vcf.gz
thal_snp_b37=/cgdata/guocq/database/gnomAD/af-only-gnomad.b37.SNP_biallelic.Thal.ip80.vcf.gz
thal_bed_b37=/cgdata/guocq/script/Thal_wf/Thal_bed_20180702.b37.bed

test -d metrics || mkdir metrics
#bed=/cgdata/guocq/script/AZF-b37/190702_AZF.merge.filter-3.b37
hg19_dict=/ngs/Bioinf/Database/ref/hg19/seq/hg19.dict
shome=/cgdata/guocq/script/AZF-b37
#$gatk BaitDesigner \
#-T Thal_bed_20180702.b37.interval_list \
#-R $b37 --DESIGN_NAME TEST_thal_120 --BAIT_OFFSET 120
#exit

test -f $bed.interval_list || \
$gatk BedToIntervalList \
-I $bed.bed \
-O $bed.interval_list \
-SD $b37_dict

exit

$gatk CollectHsMetrics \
-I $bam_dir/${sample}.bam \
-BI $bed.interval_list \
-TI $bed.interval_list \
-O metrics/${sample}_hs_metrics.txt \
-R $b37 \
--PER_TARGET_COVERAGE metrics/${sample}_hs_target.txt \
--COVERAGE_CAP 6000 -MQ 0 

cd metrics
Rscript $shome/azf_cov_norm.r $shome/AZF_ref_exon_cov-3.xls ${sample} 
perl $shome/AZF_dup_norm.pl ${sample}_norm.cov.xls
Rscript $shome/azf_seg.r ${sample}
perl $shome/AZF_del_type.pl ${sample}