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- #!/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
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