Plasmids

Plasmids:

1. replicons
2. stably inherited
3. extrachromosomal
4. double-stranded circular DNA (mostly)
5. relaxed covalently closed circles (CCC DNA), open circles (OC DNA) or supercoiled DNA
6. plasmids with unknown phenotypic traits are called cryptic plasmids
7. conjugative or non-conjugative - depending upon whether or not they carry a set of transfer genes, called the tra genes, which promote bacterial conjugation. 
8. multiple copies per cell (relaxed plasmids) or a limited number of copied per cell (stringent plasmids). 

Host range

1. Encoding only a few of the proteins required for their own replication; all the other proteins required for replication are provided by the host cell. 
2. Plasmid-encoded replication proteins are located very close to the ori (origin of replication).
3. Other parts of the plasmid can be deleted and forein sequences can be added to the plasmid and the replication can occur.  
4. The host range of a plasmid is determined by its ori region. Plasmids with a broad host range encode most, if not all, of the proteins required for replication.

Pileup Format

Pileup Format

Wiki Pileup Format

UCSC Genome Browser

The UCSC genome browser and associated tools

Guide to the UCSC Genome Browser

Hierarchical structure of UCSC Genome Browser track hub

Bash Explain Shell

Explain Shell

hs37d5.fa File Information

The missing human sequences (version 5)

Human Decoy Sequences (37d5)

The decoy genome

miRNA Temporal Analyzer

miRNA Temporal Analyzer (mirnaTA): a bioinformatics tool for identifying differentially expressed microRNAs in temporal studies using normal quantile transformation

Annotation of Non-coding Variants

SuRFing the genomics wave: an R package for prioritizing SNPs by functionality 

SuRFR Manual

VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants

Genotype Concordance Calculation

vcftools --diff

PBS Job Chains and Dependencies

PBS Job Chains and Dependencies

Problem Solving with Algorithms and Data Structures in Python

Problem Solving with Algorithms and Data Structures in Python

Plink Format to VCF Format

How to convert plink files to VCF (or other) easily parseable format?

plink_to_vcf.py (ped,map to bfile and then pseq; indirect; not recommended)

Convert PEDMAP to VCF user Kantale (the fidelity is opening to questions)

PGDSpider manual vers 2-0-7-2

VCF Summary Statistics

Summary statistics by gene/group

Core resource databases (hg19) for current release

The Downloading Link for Plinkseq

Plinkseq download link

Varint-calling Benchmarking Software

SMaSH: a benchmarking toolkit for human genome variant calling

GATK: Descriptive Statistics and Quality Control on Variants

Descriptive statistics and quality control on variants

The score that gets added to the INFO field of each variant is called the VQSLOD. It is the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.

GTAK: the Depreciation of Haloptype Scores in VQSR

"Please note that we no longer include HaplotypeScore in our recommendations for VQSR. This doe not mean you cannot use it, just that in our hands we have found it is not helpful." (Does callset derived from HyplotyperCaller need run through VariantAnnotator for VQSR step?)

GATK: NanoSchedulable / -nct vs. TreeReducible / -nt

How to make a walker compatible with multi-threading

GATK: Variant Quality Score Recalibration

(howto) Apply hard filters to a call set

Genome-Wide Linkage, Exome Sequencing and Functional Analyses Identify ABCB6 as the Pathogenic Gene of Dyschromatosis Universalis Hereditaria (a VQSR applied example)

What VQSR training sets / arguments should I use for my specific project? (QP is not recommended for the Exome-sequencing pipeline).

What does inbreedingCoeff mean?  (In relation to GATK)

Pedigree Analysis (Note that you will need at least 10 founders to compute the inbreeding coefficient.)

Variant Quality Score Recalibration (Broad Institute)

Call variations using the GATK Haplotype Caller workflow  (For Variant Quality Recalibration)

Intraclonal heterogeneity and distinct molecular mechanisms characterize the progression of t(4;14) and t(11;14) myeloma (Explanations of tranches and variant quality score recalibration).

variant calling, quality score recalibration, evaluation and filtering

Variant calling by Simon Rasmussen, 2013

GATK: Target Intervals

When should I use -L to pass in a list of intervals?

What input files does the GATK accept / require?

Visualizing the Outputs of Gatk/Depthofcoverage

Visualizing the Outputs of Gatk/Depthofcoverage