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- #!/bin/sh
- #PBS -N HLA
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate base
- hlahd_dir=/cgdata/liuxiangqiong/software/hla/hlahd.1.3.0
- target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort.bed
- export PATH=$hlahd_dir/bin:$PATH
- outputdir=${inputpath}/7HLA-HD_unpair
- cd ${outputdir}
- samtools view -hb ${bam_dir}/${sample}_clean.bam 6:28477797-33448354 | samtools sort -n |samtools fastq - -1 ${inputpath}/${sample}_partial_t1.fq -2 ${inputpath}/${sample}_partial_t2.fq
- samtools view -bh -f 4 ${bam_dir}/${sample}_clean.bam |samtools sort -n | samtools fastq - -1 ${inputpath}/${sample}_unmapped_1.fq -2 ${inputpath}/${sample}_unmapped_2.fq
- cat ${inputpath}/${sample}_partial_t1.fq ${inputpath}/${sample}_unmapped_1.fq > ${inputpath}/${sample}_part_1.fq && rm ${inputpath}/${sample}_partial_t1.fq ${inputpath}/${sample}_unmapped_1.fq
- cat ${inputpath}/${sample}_partial_t2.fq ${inputpath}/${sample}_unmapped_2.fq > ${inputpath}/${sample}_part_2.fq && rm ${inputpath}/${sample}_partial_t2.fq ${inputpath}/${sample}_unmapped_2.fq
- hlahd.sh -t 10 -m 100 -f $hlahd_dir/freq_data/ ${inputpath}/${sample}_part_1.fq ${inputpath}/${sample}_part_2.fq $hlahd_dir/HLA_gene.split.txt $hlahd_dir/dictionary ${sample} ${outputdir}
- cp ${outputdir}/${sample}/result/${sample}_final.result.txt ${outputdir}/${sample}.HLA.result.txt
- rm -rf ${inputpath}/${sample}_part_1.fq
- rm -rf ${inputpath}/${sample}_part_2.fq
- #结果处理
- python3 /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/20220705/datafile_HLA_v0_20220705_finish.py -i ${inputpath} -s ${sample}
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