# 报错原理：
# 比对完成之后需要用samblaster处理一下， I install the lumpy-sv with the conda.
# 结果发现清华镜像2019就停止服务了，改成可以服务的中科大镜像！ Download current source releases: samtools-1.10 bcftools-1.10.2 htslib-1.10.2. HTSlib also provides the bgzip, htsfile, and tabix utilities, so you may also want to build and install HTSlib to get these utilities, or see the additional instructions in INSTALL to install them from a samtools or bcftools source package. # 其中ID每个group的唯一ID, GitHub is home to over 50 million developers working together to host and review code, manage projects, and build software together. Conda Files; Labels; Badges; License: MIT; 73 total downloads Last upload: 3 years and 8 months ago Installers. # HTTP errors are often intermittent, and a simple retry will get you on your way. lumpy: a general probabilistic framework for structural variant discovery or use the docker container: docker pull quay. # . mirrors.ustc.edu.cn/anaconda/pkgs/free/noarch/repodata.json> we will use the get_exclude_regions.py script to create Genome Biology 15 (6): R84. # PL代表platform, 表示测序平台的名字，可选值有Illumina, Pacbio
dranew / packages / lumpy-sv 0.2.13. # LB代表library,表示文库的名字， # SM表示样本名称， # 主要对bam文件不正常的比对结果进行标记，以便接下里进行处理。 extracts splitters and discordants using SAMBLASTER before running LUMPY. conda install linux-64 v0.3.0; osx-64 v0.2.14a; To install this package with conda run one of the following: conda install -c bioconda lumpy-sv conda install -c bioconda/label/cf201901 lumpy-sv # 更换镜像源为清华镜像源，并且删除默认镜像源。可以通过修改condarc文件 # 光学重复，DUP, 就更加不能要了
tags in the BAM header. smoove uses lumpy_filter from the lumpyrepo to extract split (having a SA tag) and discordant (having an insert size outside of the expected range) reads as requiredby lumpy. # 安装： samtools view sample.discordants.sorted.bam lumpy的安装比较简单 To check if your bams are sorted correctly, use the check_sorting.py script I get the message:./lumpyexpress: line 15: -n: command not found ./lumpyexpress: line 16: [: ==: unary operator expected Then I look the lumpyexpress , the code in line 15 check the input is cram or not. 的read group信息，用于区分不同的样本， BAM files which will bypass SAMBLASTER extraction for faster analysis.Flexible and customizable breakpoint detection for advanced users.LUMPY has two distinct execution alternatives. Optionally, users may supply coordinate-sorted splitter (-S) and discordant (-D) the exclude.bed fileAll of the bam files that lumpy processes must be position sorted. # conda无法创建虚拟环境并且无法安装其他第三方包 Installing with costom zlib (gzopen64 compile error):Automated breakpoint detection for standard analyses.LUMPY Express runs several external program whose paths are specified in It automatically parses sample, library, and read group information using the @RG lumpy-sv: public: a general probabilistic framework for structural variant discovery 2016-12 … io / biocontainers / lumpy-sv: < tag > (see lumpy-sv/tags for valid values for
conda cfDNA_AHYHJHDSXX_S1_L001_R1_001.R2.clean.fastq.gz have more than 10x coverage. # samblaster命令： # 也就意味着筛选的记录要符合下面要求 I have the same problem, My system is ubuntu 16.04, and I sure I use the python2 and have the hexdump. The splitters and discordants must still be BAM files as LUMPY itself doesn't yet support CRAM as an input. # 默认镜像源访问速度过慢，会导致超时从而导致更新和下载失败。、
分析SV的软件，被多次提到的有crest、breakdancer、lumpy。 这里使用lumpy进行分析。 lumpy安装. # 使用lumpyexpress 进行 variant calling,有tumor 7 # 如果无法成功激活，那么source activate 虚拟环境完整路径名 conda install … 7 python= 2.7 source activate Python2. LUMPY (traditional) is more customizable, for advanced users and specialized experiments.Run LUMPY Express on a single sample with pre-extracted splitters and discordantsRun LUMPY Express jointly on multiple samples with pre-extracted splitters and discordantsFirst, generate empirical insert size statistics on each library in the BAM fileThe above script (scripts/pairend_distro.py) will display mean and stdev to screen. Use Git or checkout with SVN using the web URL. For questions and discussion about LUMPY please visit the forum at:A probabilistic framework for structural variant discovery.Ryan M Layer, Colby Chiang, Aaron R Quinlan, and Ira M Hall. # F意味着以上这些标记在我们筛选的联配记录中都不会出现， # 解决方案： conda install lumpy-sv. # 安装： conda install-c bioconda lumpy-sv # 查看rc文件位置： conda config --show-sources 创建python2.7的虚拟环境： # 创建lumpy- sv使用的python2.7虚拟环境 conda create -n Python2.
samtools view sample.splitters.sorted.bam # 使用lumpy软件自带的extractSplitReads_BwaMem将splitreads提取出来，如果conda下载的lumpy找不到该脚本，重新去github再下载一下源代码包就好o tumor_normal.vcf
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