#!/bin/sh
#PBS -N HL
#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
snp_target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/HL_227_b10.bed
site=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/HL_227_norm.vcf.gz
gene=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/HL_gene_VS_rs.tab
#bamdir=.
#sample=$1
#outdir=.
outdir=${inputpath}/5HL_gatk_unpair
$gatk4 HaplotypeCaller -R $b37 -I  ${bam_dir}/${sample}_clean.bam --genotyping-mode GENOTYPE_GIVEN_ALLELES -L $snp_target --alleles $site -O $outdir/${sample}.HL.vcf
perl /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/trim_HL_site.pl $site $gene $outdir/${sample}.HL.vcf > $outdir/${sample}.HL.xls

#进行结果处理
python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_chemotherapy_v0_20220705_finish.py -i ${inputpath} -s ${sample}