#!/bin/sh
#PBS -N Germline
#PBS -j oe
#PBS -l ncpus=12
#PBS -l nodes=1
#PBS -l mem=20G

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
gatk4=/cgdata/CGTools/soft/tools/gatk4/gatk-4.0.8.1/gatk
b37=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort_NOhap.bed
annovar_dir=/cgdata/soft/src/annovar.archive/annovar_v20200608
annovar_db=/cgdata/soft/src/annovar.archive/annovar_v20200608/DB

outdir=${inputpath}/4Germline_unpair
$gatk4 HaplotypeCaller -R $b37 -I ${bam_dir}/${sample}_clean.bam -ip 50 -L ${target}  -O ${outdir}/${sample}.vcf.gz
perl $annovar_dir/table_annovar.pl  ${outdir}/${sample}.vcf.gz $annovar_db \
    -buildver hg19 -out ${outdir}/${sample} -remove \
    -protocol refGene,genomicSuperDups,phastConsElements46way,omim,avsnp150,clinvar,icgc28,cosmic94,gnomad_exome,1000g2015aug_all,hgmd-pro,intervar_20180118,dbscsnv11,dbnsfp41a,regsnpintron \
    -operation g,r,r,r,f,f,f,f,f,f,f,f,f,f,f  \
    -nastring . -vcfinput -polish
perl /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/germ_filter.pl -i ${outdir}/${sample}.hg19_multianno.txt -s /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/Select_RefSeq_HGNC_MANE.txt ${outdir}/${sample}.germ.xls