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- #!/bin/sh
- #PBS -N align_noUMI
- #PBS -j oe
- #PBS -l ncpus=20
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate base
- hg19=/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.bed
- #################################################################################1.trim#########################################################
- runstart="`date '+%F%n%T'`"
- echo ${sample} "start at" $runstart
- echo "#--------------------------------------STEP1.clean the raw data--------------------------------------#"
- starttime="`date '+%Y%m%d%H%M%S'`"
- #fastp -i ${inputpath}/${sample}_R1.fastq.gz -I ${inputpath}/${sample}_R2.fastq.gz -o ${inputpath}/${sample}_clean_R1.fq.gz -O ${inputpath}/${sample}_clean_R2.fq.gz -c -l 50 -q 20 --umi --umi_loc read1 --umi_len 8 -j ${inputpath}/${sample}.fastp.json -h ${inputpath}/${sample}.fastp.html
- fastp -i ${inputpath}/${sample}_R1.fastq.gz -I ${inputpath}/${sample}_R2.fastq.gz -o ${inputpath}/${sample}_clean_R1.fq.gz -O ${inputpath}/${sample}_clean_R2.fq.gz -c -l 50 -q 20 -j ${inputpath}/${sample}.fastp.json -h ${inputpath}/${sample}.fastp.html
- echo "#--------------------------------------STEP1.clean the raw data finished!---------------#"
- #################################################################################2.mapping#########################################################
- #2.1.speedseq align
- echo "#--------------------------------------STEP2.align to refdata--------------------------------------#"
- speedseq align -t 40 -o ${bam_dir}/${sample}_clean -R "@RG\tID:${sample}\tSM:${sample}\tLB:${sample}" ${hg19} ${inputpath}/${sample}_clean_R1.fq.gz ${inputpath}/${sample}_clean_R2.fq.gz
- echo "#--------------------------------------STEP2.align to refdata finished!--------------------------------------#"
- rm -rf ${bam_dir}/${sample}_clean.splitters.bam
- rm -rf ${bam_dir}/${sample}_clean.splitters.bam.bai
- rm -rf ${bam_dir}/${sample}_clean.discordants.bam
- rm -rf ${bam_dir}/${sample}_clean.discordants.bam.bai
- endtime="`date '+%Y%m%d%H%M%S'`"
- echo "step1 run " $[$endtime-$starttime]"s">${inputpath}/${sample}_mapping.log
- echo "${sample} mapping finish!" >>${inputpath}/${sample}_mapping.log
- echo "#--------------------------------------STEP3.qualimap--------------------------------------#"
- ourputdir=${inputpath}/9Ontarget
- samtools flagstat ${bam_dir}/${sample}_clean.bam > ${ourputdir}/${sample}_clean.abra2.flagstat
- #cd ${ourputdir}
- #qualimap bamqc -bam ${bam_dir}/${sample}_clean.bam -c --java-mem-size=40G -gff ${target}
- #去掉dup
- qualimap bamqc -bam ${bam_dir}/${sample}_clean.bam -c -sd --java-mem-size=40G -gff ${target}
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