官方脚本模板：
gatk Mutect2 \
-R reference.fa \
-I sample.bam \
--germline-resource af-only-gnomad.vcf.gz \
--panel-of-normals pon.vcf.gz \
-O single_sample.vcf.gz构建批量代码
ls ../align/*_bqsr.bam | perl -ne 'chomp; if($_ =~ /([^\/]+)_bqsr\.bam/) { print "gatk --java-options \"-Xmx20G -Djava.io.tmpdir=./\" Mutect2 -R /data02/zhangmengmeng/database/hg38/hg38.fa -I ../align/$1_bqsr.bam -L /data02/zhangmengmeng/database/gatk_resource_bundle/hg38/AgilentV6_GRCh38_ex_region.sort.bed --germline-resource /data02/zhangmengmeng/database/gatk_resource_bundle/hg38/somatic-hg38_af-only-gnomad.hg38.vcf.gz --panel-of-normals /data02/zhangmengmeng/database/gatk_resource_bundle/hg38/somatic-hg38_1000g_pon.hg38.vcf.gz --f1r2-tar-gz $1.f1r2.tar.gz --O $1.raw.vcf && gatk LearnReadOrientationModel -I $1.f1r2.tar.gz -O $1.read-orientation-model.tar.gz && gatk GetPileupSummaries -I ../align/$1_bqsr.bam -L /data02/zhangmengmeng/database/gatk_resource_bundle/hg38/AgilentV6_GRCh38_ex_region.sort.bed -V /data02/zhangmengmeng/database/gatk_resource_bundle/hg38/somatic-hg38_af-only-gnomad.hg38.vcf.gz -O $1.pileups.table && gatk CalculateContamination -I $1.pileups.table -O $1.CalculateContamination.table && gatk FilterMutectCalls -R /data02/zhangmengmeng/database/hg38/hg38.fa -V $1.raw.vcf --contamination-table $1.CalculateContamination.table --ob-priors $1.read-orientation-model.tar.gz -O $1.somatic.vcf && gatk FilterAlignmentArtifacts -R /data02/zhangmengmeng/database/hg38/hg38.fa --bwa-mem-index-image /data02/zhangmengmeng/database/hg38/hg38.fa.img -V $1.somatic.vcf -O $1.somatic.FAA.vcf -I ../align/$1_bqsr.bam && awk \x27/^#/ {print \$0; next} \$7==\x22PASS\x22 {print \$0}\x27 $1.somatic.FAA.vcf > ./$1.somatic.passed.vcf && echo $1 ok\n" }' > mutect2_TumorOnly.sh