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- #!/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}
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