#!/bin/sh
#PBS -N coverage
#PBS -j oe
#PBS -l ncpus=20
#PBS -l nodes=1
#PBS -l mem=40G

#inputpath=$1
#sample=$2
source  /home/liuxiangqiong/miniconda3/bin/activate base
target=/cgdata/liuxiangqiong/work62pancancer/pipeline/v0/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
outputdir=${inputpath}/10Coverage
#5.计算每个位点的测序深度
#也可用samtools depth.但是需要注意设置上线。
samtools depth -d 20000 -b ${target} ${bam_dir}/${sample}_clean.bam >${outputdir}/${sample}.cov.samtools.txt
#计算每个探针的平均覆盖深度
python3 /cgdata/liuxiangqiong/work62pancancer/pipeline/v0/noUMI_v0/sample_coverage_v0_20220906.py -i ${inputpath} -s ${sample}
#采用bedtools分析，可能会出错
#bedtools coverage -d -a ${target} -b  ${bam_dir}/${sample}_clean.bam >${outputdir}/${sample}_clean_abra2_target_cov.txt
#bamdir=/cgdata/pancancer/analyse/lane7/bamfile/${sample}_clean.bam

###采用fgbio计算测序错误率
#outputdir2=${inputpath}/8Fastqc
#fgbio=/cgdata/liuxiangqiong/software/fgbio/fgbio-1.3.0.jar
#ref=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
#dbsnp138=/cgdata/Database/GATK/b37/dbsnp_138.b37.vcf
#java -jar $fgbio ErrorRateByReadPosition -i ${bam_dir}/${sample}_clean.bam --collapse=false -r $ref -v $dbsnp138 -o $outputdir2/$sample