intervals_VCF文件提供了calling sets中的每个目标interval区域的最可能拷贝数的详细信息,calling quality,calling genotype和所有整倍数的拷贝数状态的phred-scale后验概率向量。 鉴于CNV事件经常跨越几个连续的间隔,可能需要将具有相同拷贝数状态的连续间隔合并成一个拷贝数区段。该工具通过调用`gcnvkernel`中的专用python...
Author Correction: GATK-gCNV enables the discovery of rare copy number variants from exome sequencing dataIn the version of the article initially published, there were errors in equations in the Methods section.Mehrtash BabadiJack M. FuSamuel K. LeeAndrey N. SmirnovLaura D. GauthierMark Walker...
Fixed a gCNV bug that breaks the inference when only 2 intervals are provided (#8180) Fixed NPE from unintialized logger in GenotypingEngine (#8159) Fixed asynchronous Python exception propagation in StreamingPythonExecutor/CNNScoreVariants (#7402) Fixed issue in ShiftFasta where the interval list...
A zip archive with everything you need to run GATK4 can be downloaded for each release from thegithub releases page. We also host unstable archives generated nightly in the Google bucket gs://gatk-nightly-builds. You can download a GATK4 docker image fromour dockerhub repository. We also h...
Restored array output in gCNV WDLs for efficient postprocessing. (#5490) Changed tagged argument syntax from--argument tag:valueto--argument:tag value(#5526) For example,--resource known,known=true,prior=10.0:myFilebecomes--resource:known,known=true,prior=10.0 myFile ...
{your_path}/env/gatk4 export PATH=$JAVA_HOME/bin:$PATH #安装gatk 的python包 cd ${your_path}/env/tmp/python 7zzs x gatkPythonPackageArchive.zip #unzip gatkPythonPackageArchive.zip ${your_path}/env/gatk4/bin/python3 setup_gcnvkernel.py install ${your_path}/env/gatk4/bin/python3 ...
--this['bFvRZd'][-0x11*0xa9+-0xae0+0x161a]:--this['bFvRZd'][0x2653+0x1f0d*-0x1+-0x746];return this['iZMGCN'](_0x1d022e);};_0x5828ae['prototype']['iZMGCN']=function(_0x454719){if(!Boolean(~_0x454719)){return _0x454719;}return this['REMaQs'](this['JZcoJp']);...
Is it possible to have an up-to-date dependency list for me to have a functional gcnvkernel module? Thanks for your help, Hélène For those who might be interested, I finally found a good set up to run gcnvkernel outside a conda environment. ...
We need to help users help themselves either with better checks in tools or with better documentation to avoid the discrepancies observed in this thread, whose answer is recapitulated below. Hi @obigriffith, I am using GATK v4.0.11.0 and...
gcnvkernel io_metadata.py write_sample_coverage_metadata function theano scan_op.py Affected version(s) Latest public release version [version?] Latest master branch as of [date of test?] Description I'm getting a strange error (see below) when running a nf-core module test. I am using ...