通過AGS調用mutect2任務來檢測體細胞短突變，短突變包括單核苷酸（SNV）以及插入和缺失（InDel）的突變。本文介紹如何通過AGS分析腫瘤樣本。
背景資訊
AGS mutect2支援兩種模式的典型情境：
腫瘤加正常樣本模式：腫瘤樣本在分析過程跳過正常人的胚系變異。
腫瘤模式：對單個腫瘤樣本的比對資料進行分析。
mutect2的體系變異檢測是保持了和GATK4.1.3一致的變異檢測方式，但提供了30~80倍的加速。針對90Gbase的比對資料，10分鐘內可以完成變異檢測。
mutect2使用樣本
以下操作將為您示範如何通過命令檢測AGS Mutect2腫瘤。
在腫瘤加正常樣本模式下分析樣本
以給定匹配的正常樣本作為基準，mutect2僅檢測體細胞變異。mutect2會根據提供的證據（例如在匹配的正常樣本中），實現跳過在胚系中明顯存在的變異的邏輯，以避免在胚系事件上花費計算資源。
用法
執行命令：
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預期輸出：
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 | +--------------------------+---------------------------+
在單獨腫瘤樣本模式下分析樣本
此模式對單一類型的樣本（例如腫瘤或正常樣本）進行分析。
用法
執行命令：
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預期輸出：
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 | +--------------------------+-------------------------+