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

单击检测AGS Mutect2肿瘤,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(例如在匹配的正常人中),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 \
    返回结果:
    --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
  • 结果示例:
    --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 \
    返回结果:
    --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
  • 结果示例:
    --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                       |
    +--------------------------+-------------------------+