zoukankan      html  css  js  c++  java
  • WES分析--call SNV--Mutect2

    1. 生成fai和dict文件:

    java -Xmx50g -jar picard.jar CreateSequenceDictionary R=/home/dklv/GW/software/bwa.kit-0.7.15_x64-linux/index_gencode_hg38/GRCh38.primary_assembly.genome.fa O=/home/dklv/GW/software/bwa.kit-0.7.15_x64-linux/index_gencode_hg38/GRCh38.primary_assembly.genome.dict

    samtools faidx GRCh38.primary_assembly.genome.fa

    以上参考:https://gatkforums.broadinstitute.org/gatk/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference

    2. 修改bam文件中的RG信息:

    java -Xmx50g -jar picard.jar AddOrReplaceReadGroups ID=B1 PL=illumina LB=LaneX PU=NONE SM=B1 INPUT=$tbam OUTPUT=B1.bam

    此步是可以避免的,如果在map时,就把RG信息设置好。

      RG的解释:This tag identifies which read group each read belongs to, so each read group's ID must be unique. It is referenced both in the read group definition line in the file header (starting with @RG) and in the RG:Z tag for each read record. (参考:https://gatk.broadinstitute.org/hc/en-us/articles/360035890671?id=11015)

      所以,一定要将设置好RG的ID!!

    3.

    ./gatk --java-options "-Xmx40g" Mutect2  -R $fa -I $tbam -tumor $tbam --disable-read-filter MateOnSameContigOrNoMappedMateReadFilter -O 1_PC.vcf.gz

    参考:

    https://gatk.broadinstitute.org/hc/en-us/articles/360037224712--Tool-Documentation-Index(GATK所有工具的汇总,点击其中Mutect2可进入该工具的tutorial)

    https://gatk.broadinstitute.org/hc/en-us/articles/360035531132(该网址mutect2的tutorial网址)

    https://gatk.broadinstitute.org/hc/en-us/articles/360035889791?id=11136#2(该网址是mutect2的tutorial,虽然标注为deprecatd,但我觉得此网址比上面的tutorial网址详细。)

    https://gatk.broadinstitute.org/hc/en-us/articles/360035889791?id=11136#2 的“Create a sites-only PoN with CreateSomaticPanelOfNormals”。

  • 相关阅读:
    C++内联函数
    C++类中创建线程
    windows下搭建Redis集群
    tcpdump截帧工具使用
    使用gdb调试应用程序
    工作之用
    primecoin服务常用命令和参数说明
    Windows mysql默认字符集修改
    primecoin在ubuntu16.04上部署服务:
    ubuntu磁盘分配和挂载
  • 原文地址:https://www.cnblogs.com/zypiner/p/12689167.html
Copyright © 2011-2022 走看看