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- #!/bin/sh
- #PBS -N Germline
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate base
- gatk4=/cgdata/CGTools/soft/tools/gatk4/gatk-4.0.8.1/gatk
- b37=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- target=/cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/NanOnco_Plus_Panel_v2.0_Covered_b37_cg.parY2X.sort_NOhap.bed
- annovar_dir=/cgdata/soft/src/annovar.archive/annovar_v20200608
- annovar_db=/cgdata/soft/src/annovar.archive/annovar_v20200608/DB
- outdir=${inputpath}/4Germline_unpair
- $gatk4 HaplotypeCaller -R $b37 -I ${bam_dir}/${sample}_clean.bam -ip 50 -L ${target} -O ${outdir}/${sample}.vcf.gz
- perl $annovar_dir/table_annovar.pl ${outdir}/${sample}.vcf.gz $annovar_db \
- -buildver hg19 -out ${outdir}/${sample} -remove \
- -protocol refGene,genomicSuperDups,phastConsElements46way,omim,avsnp150,clinvar,icgc28,cosmic94,gnomad_exome,1000g2015aug_all,hgmd-pro,intervar_20180118,dbscsnv11,dbnsfp41a,regsnpintron \
- -operation g,r,r,r,f,f,f,f,f,f,f,f,f,f,f \
- -nastring . -vcfinput -polish
- perl /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/germ_filter.pl -i ${outdir}/${sample}.hg19_multianno.txt -s /cgdata/liuxiangqiong/work62pancancer/Client/v0/script/refdata/Select_RefSeq_HGNC_MANE.txt ${outdir}/${sample}.germ.xls
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