pcgr
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sigven
Personal Cancer Genome Reporter (PCGR)
Opening this issue to keep track of our efforts to handle the PCGR conda installation within a single conda environment, as opposed to two separate Python and R-based ones which...
When fed with vcf files from GATK4(version gatk-4.0.1.2) Mutect2, I got error message: 2018-04-26 12:37:19 - pcgr-validate-input - ERROR - According to the VCF specification, the VCF file (/workdir/input_vcf/AE188.mutect2.vcf.gz) is...
Hi sigven, The "fusion" evidences providing function is not added to the PCGR (v0.9.1) we are using, so we develop and use our own script to provide the evidences. Could...
Thanks for the great tool - very useful! Do you think there would be any chance of a summary HTML across a cohort of samples that have been through PCGR?
Is it possible to specify the `name` of the tumor sample in the VCF, and then for pcgr to extract `AF`, `DP` from that column? Do you a recommended approach,...
Hi, Sigven, Now PCGR can analysis SNV/INDEl and CNA. would you like to add gene fusion function in the future? Another question is that given tumor/normal raw data(fastq), can you...
Reporting this issue we got via email: ``` Preparing transaction: done Verifying transaction: done Executing transaction: done ERROR conda.core.link:_execute(730): An error occurred while installing package 'bioconda::bioconductor-genomeinfodbdata-1.2.7-r41hdfd78af_1'. Rolling back transaction: done...
Hello, I have been running PCGR (v1.4.1, GRCh37) on some clinical samples. These were just tests, so I didn't use proper pipelining workflows. I just used ```xargs``` to run samples...
Reporting this conda installation issue we got via email: ``` Downloading and Extracting Packages Preparing transaction: done Verifying transaction: failed [Errno 40] Too many levels of symbolic links: '[...]/miniconda3/pkgs/ncurses-6.2-h58526e2_4/share/terminfo/N/NCR260VT300WPP' ```...