to doz

[snewhouse]

Scratch pad

hs38 primary assembly of GRCh38 (incl. chromosomes, unplaced and unlocalized contigs) and EBV
hs38a hs38 plus ALT contigs
hs38DH hs38a plus decoy contigs and HLA genes (recommended for GRCh38 mapping)
hs37 primary assembly of GRCh37 (used by 1000g phase 1) plus the EBV genome
hs37d5 hs37 plus decoy contigs (used by 1000g phase 3)

For 1.0 to 1.X

ploidy options - freebayes
SEX chrom calling XX XY Y
lcr regions options
config file reading in fixes
config file order of options
platypus options testing and tweaks
test freebayes options - regions are mapped reads callable loci or just Chromsomes
Improve logging
clean up install
biobambam

Future Dev

b38 indexes - GIAB
b38 pipelines - GIAB
gui - user install updates git AWS gce pricing registration for GATK and others
capture bed files from companies
recalling pipeline
cohort pipeline
cancer pipeline
CNV pipeline
Annotation pipeline
PGRS pipeline plus reporting
chanjo
bcbio options : give user option for bcbio or speedseq
test speedseq
need parser to create options for calling bcbio or speedseq

Browsers

http://genomesavant.com/p/savant/index

[snewhouse]

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

[snewhouse]

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

[snewhouse]

# 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 \
   | sed 's/ID=AD,Number=./ID=AD,Number=R/'
   | vt decompose -s - \
   | vt normalize -r $REF - \
   | java -Xmx4G -jar $SNPEFFJAR -formatEff -classic GRCh37.75  \
   | bgzip -c > $NORMVCF
tabix $NORMVCF

[snewhouse]

Add decoy genomes

EBV
Human pathogens

[snewhouse]

Add SURPI

[snewhouse]

GATK 3

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

[snewhouse]

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 Pritchard, Yaniv Erlich

doi: http://dx.doi.org/10.1101/017459

Abstract

Expression quantitative trait loci (eQTLs) are a key tool to dissect cellular processes mediating complex diseases. However, little is known about the role of repetitive elements as eQTLs. We report a genome-wide survey of the contribution of Short Tandem Repeats (STRs), one of the most polymorphic and abundant repeat classes, to gene expression in humans. Our survey identified 2,060 significant expression STRs (eSTRs). These eSTRs were replicable in orthogonal populations and expression assays. We used variance partitioning to disentangle the contribution of eSTRs from linked SNPs and indels and found that eSTRs contribute 10%-15% of the cis-heritability mediated by all common variants. Functional genomic analyses showed that eSTRs are enriched in conserved regions, co-localize with regulatory elements, and are predicted to modulate histone modifications. Our results show that eSTRs provide a novel set of regulatory variants and highlight the contribution of repeats to the genetic architecture of quantitative human traits.

[snewhouse]

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

[afolarin]

userns has been dropped from Docker 1.7. Trying to find out when it is penned in (hopefully v1.8)

[snewhouse]

better logging
cleanups

[snewhouse]

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 Genomes Project and SV companions 

maps using next-generation sequencing.”, Nature Genetics, 2009

(2010,2011,2012,2015), Great Ape Diversity Project (Prado-Martinez et al, Nature, 2013), 

several genome projects (gorilla, bonobo), Neandertal and Denisova projects, dog 

domestication (Freedman et al, 2014), cat domestication (Montague et al, 2014 and 

Tamazian et al 2014), maybe others...

MetaSV: an accurate and integrative structural-variant caller for next generation sequencing.

[snewhouse]

http://mrcanavar.sourceforge.net/

mrCaNaVaR (mɪstər ʤʌnʌvʌr) is a copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals.

[snewhouse]

vt peek v0.5

description : Summarizes the variants in a VCF file

usage : vt peek [options] <in.vcf>

options : -y  output pdf file [summary.pdf]
          -x  output latex directory []
          -f  filter expression []
          -I  file containing list of intervals []
          -i  intervals []
          -r  reference sequence fasta file []
          -?  displays help