(howto) Install and run Oncotator for the first time
1. Download the Oncotator package, the default datasources package, and (recommended) transcript override list from the Downloads page Please note: Broadies who wish to run the installed Oncotator on...
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Unboxing GATK4
This is one of two posts announcing the imminent beta release of GATK4; for details about the open-source licensing, see this other post. You've probably heard it by now: we are on the cusp of...
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View ArticleUsing GenomeStrip to genotype known vcf
Hi, I want to genotype known CNVs (from 1000G Phase3, GoNL, etc.) in our samples using GenomeStrip without performing any discovery step at first. 1) Do I have to run only the SVPreprocess steps...
View ArticleGATK 4.0 will be released Jan 9, 2018
A long time ago in a galaxy far, far away, we started work on a brand new version of GATK in which the engine framework was to be completely revamped, streamlined and accelerated, with support for...
View ArticleAre you going to have a working version in few time of the complete GATK Best...
I am trying to use your Spark commands in GATK 4 release in order to execute the GATK Best Practices with Spark and it looks working fine until the BQSRPipelineSpark (I am using...
View Articlefinal result
The question is that after running GenotypeGVCF, and getting VCF file then how we can get the result for every sample we have run GenotypeGVCF. I mean if we run haplotyping for 100 samples and getting...
View Articleabout genotypegvcfs
I want to know about the algorithm which converts raw gVCF files from different samples to raw VCF by doing genotypegvcfs
View ArticleWhat are the differences in using default and custom interval list (-L) for...
I mean to say default interval list (-L) as exome region and custom interval list as designed and given by the company like agilent or illumina. What will the difference in the output generated using...
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