通过AGS调用mutect2任务来检测体细胞短突变，短突变包括单核苷酸（SNV）以及插入和缺失（InDel）的突变。本文介绍如何通过AGS分析肿瘤样本。
背景信息
AGS mutect2支持两种模式的典型场景：
肿瘤加正常样本模式：肿瘤样本在分析过程跳过正常人的胚系变异。
肿瘤模式：对单个肿瘤样本的比对数据进行分析。
mutect2的体系变异检测是保持了和GATK4.1.3一致的变异检测方式，但提供了30~80倍的加速。针对90Gbase的比对数据，10分钟内可以完成变异检测。
mutect2使用示例
以下操作将为您演示如何通过命令检测AGS Mutect2肿瘤。
在肿瘤加正常样本模式下分析样本
以给定匹配的正常样本作为基准，mutect2仅检测体细胞变异。mutect2会根据提供的证据（例如在匹配的正常样本中），实现跳过在胚系中明显存在的变异的逻辑，以避免在胚系事件上花费计算资源。
用法
执行命令：
ags remote run mutect2 \ --region cn-shenzhen # region of oss, e.g. cn-shenzhen, cn-beijing and etc\ --bucket my-test-shenzhen # Bucket name\ --input-bam-tumor bam/HKU2_160660.bam #Tumor sample bam file\ --input-bam-normal bam/MGISEQ_NA12878_RG_HG38.bam # Optional normal sample bam \ --bed bed/performance.blocks.exp.bed # Optional target bed \ --output-vcf vcf/HKU2_160660.vcf # Output filename\ --service "s" #SLA: [n:normal|s:silver|g:gold|p:platinum]\ --reference [hg19|hg38|<reference path on OSS>] # hg19: it is hs37d5 version, GRCh37/hg19 include decoy contig, no support for UCSC hg19. hg38: GRCh38/hg38 include decoy预期输出：
ags remote run mutect2 \ --region cn-shenzhen \ --bucket my-test-shenzhen \ --input-bam-tumor bam/HKU2_160660.bam \ --input-bam-normal bam/MGISEQ_NA12878_RG.bam \ --output-vcf vcf/HKU2_160660.vcf \ --service "s" \ --reference hg19 INFO[0001] {"JobName":"mutect2-gpu-vp7d9"} INFO[0001] Job submit succeed ags remote get mutect2-gpu-vp7d9 --show +-------------------+------------------+---------+-------------------------------+---------------+-------------+-------------+ | JOB NAME | JOB NAMESPACE | STATUS | CREATE TIME | DURATION | TOTAL READS | TOTAL BASES | +-------------------+------------------+---------+-------------------------------+---------------+-------------+-------------+ | mutect2-gpu-vp7d9 | XXXXXXXXX | Running | 2020-04-10 16:02:39 +0800 CST | 36.311883677s | 0 | 0 | +-------------------+------------------+---------+-------------------------------+---------------+-------------+-------------+ +--------------------------+---------------------------+ | JOB DETAIL | | +--------------------------+---------------------------+ | mutect2_reference_group | | | mutect2_oss_region | cn-shenzhen | | mutect2_bucket_name | my-test-shenzhen | | mutect2_output_vcf_name | vcf/HKU2_160660.vcf | | mutect2_reference_file | hg19 | | mutect2_input_bam_tumor | bam/HKU2_160660.bam | | mutect2_input_bam_normal | bam/MGISEQ_NA12878_RG.bam | | mutect2_input_bed | | | mutect2_service | s | +--------------------------+---------------------------+
在单独肿瘤样本模式下分析样本
此模式对单一类型的样本（例如肿瘤或正常样本）进行分析。
用法
执行命令：
ags remote run mutect2 \ --region cn-shenzhen # region of oss, e.g. cn-shenzhen, cn-beijing and etc\ --bucket my-test-shenzhen # Bucket name\ --input-bam-tumor bam/HKU2_160660.bam #Tumor／Normal sample bam file\ --output-vcf vcf/HKU2_160660.vcf # Output filename\ --service "s" #SLA: [n:normal|s:silver|g:gold|p:platinum]\ --reference [hg19|hg38|<reference path on OSS>] # hg19: it is hs37d5 version, GRCh37/hg19 include decoy contig, no support for UCSC hg19. hg38: GRCh38/hg38 include decoy预期输出：
ags remote run mutect2 \ --region cn-shenzhen \ --bucket my-test-shenzhen \ --input-bam-tumor bam/HKU2_160660.bam \ --output-vcf vcf/HKU2_160660.all.vcf \ --service "s" \ --reference hg19 INFO[0001] {"JobName":"mutect2-gpu-6tc8s"} INFO[0001] Job submit succeed ags remote get mutect2-gpu-6tc8s --show +-------------------+------------------+-----------+-------------------------------+----------+-------------------------------+-------------+-------------+ | JOB NAME | JOB NAMESPACE | STATUS | CREATE TIME | DURATION | FINISH TIME | TOTAL READS | TOTAL BASES | +-------------------+------------------+-----------+-------------------------------+----------+-------------------------------+-------------+-------------+ | mutect2-gpu-6tc8s | XXXXXXXXXX | Succeeded | 2020-04-10 15:51:59 +0800 CST | 4m12s | 2020-04-10 15:56:11 +0800 CST | 0 | 0 | +-------------------+------------------+-----------+-------------------------------+----------+-------------------------------+-------------+-------------+ +--------------------------+-------------------------+ | JOB DETAIL | | +--------------------------+-------------------------+ | mutect2_oss_region | cn-shenzhen | | mutect2_input_bam_tumor | bam/HKU2_160660.bam | | mutect2_input_bam_normal | | | mutect2_input_bed | | | mutect2_output_vcf_name | vcf/HKU2_160660.all.vcf | | mutect2_bucket_name | my-test-shenzhen | | mutect2_reference_file | hg19 | | mutect2_reference_group | | | mutect2_service | s | +--------------------------+-------------------------+