Stephen J Newhouse

ADD https://github.com/GregoryFaust/yaha

``` vt decompose -s $VCF | vt normalize -r $REFERENCE - > $NEW_VCF ``` change var calling to use above ; sub vcfallelicprimitives for vt decompose see http://gemini.readthedocs.org/en/latest/content/preprocessing.html

``` bash # decompose, normalize and annotate VCF with snpEff. # NOTE: can also swap snpEff with VEP #NOTE: -classic and -formatEff flags needed with snpEff >= v4.1 zless $VCF...

# Add decoy genomes EBV Human pathogens

**Add SURPI**

## GATK 3 add options and scripts for HC gVCF stuff (1.5 or 2.0 release)

# lobSTR #### Abundant contribution of short tandem repeats to gene expression variation in humans Melissa Gymrek, Thomas Willems, Haoyang Zeng, Barak Markus, Mark J Daly, Alkes L Price, Jonathan...

mention I doc that ngseasy is run as NON-ROOT within the container. Docker 1.7 should have namespace

better logging cleanups

mr and mrs Fast mrCaNaVaR ``` Alkan et al, “Personalized copy number and segmental duplication maps using next-generation sequencing.”, ● Also used in: ○ Sudmant et al, Science, 2010; 1000...