AGS無服務化分析基因數據
通過調用AGS的遠程任務，可以完成一序列的基因數據的二級分析，不需要申請和持有云計算資源，就可以完成對海量數據的批量處理，目前可以支持人類全基因組，外顯子，基因比對，宏基因組比對，Somatic胚系變異發現等業務場景的加速和低成本處理。詳細使用方式參考AGS服務
ags remote run --help
run aliyun custom process
Usage:
ags remote run [flags]
ags remote run [command]
Available Commands:
hc HaplotypeCaller job for haplotypes
mapping mapping job, it is equal to a combination of "bwa aln, bwa sampe, samtools sort, gatk MarkDuplicates "
mutect2 mutect2 job for somatic variant
rna-mapping mapping job for virus
wgs end to end job of mapping and HaplotypeCaller for WGS, WES and so on通過AGS分析腫瘤樣本
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)的改變。本文介紹如何通過AGS分析腫瘤樣本。
背景信息
AGS mutect2 支持兩種模式的典型場景：
- 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數據進行分析。
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的比對數據，10分鐘內可以完成變異檢測。
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（例如在匹配的正常人中），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：
Usage:
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
e.g：
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
Usage:
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
e.g.
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 |
+--------------------------+-------------------------+
