Message Correlation.; 7 minutes to read; Contributors. All; In this article. This sample demonstrates how a Message Queuing (MSMQ) application can send an MSMQ message to a Windows Communication Foundation (WCF) service and how messages can be correlated between sender and receiver applications in a request/response scenario. Speaking of philosophers, David Hume argued that causation doesn't exist in any provable sense. Karl Popper and the Falsificationists maintained that we cannot prove a relationship, only disprove it, which explains why statistical analyses do not try to prove a correlation; instead, they pull a double negative and disprove that the data are uncorrelated, a process known as rejecting the null.
VCF file structureA VCF file can be thought of as having three sections: a vcf header, a fix region and a gt region. The VCF meta region is located at the top of the file and contains meta-data describing the body of the file. Each VCF meta line begins with a ‘##’. The information in the meta region defines the abbreviations used elsewhere in the file. It may also document software used to create the file as well as parameters used by this software. Below the metadata region, the data are tabular. The first eight columns of this table contain information about each variant.
This data may be common over all variants, such as its chromosomal position, or a summary over all samples, such as quality metrics. These data are fixed, or the same, over all samples. The fix region is required in a VCF file, subsequent columns are optional but are common in our experience.
Beginning at column ten is a column for every sample. The values in these columns are information for each sample and each variant. The organization of each cell containing a genotype and associated information is specified in column nine, the FORMAT column. The location of these three regions within a file can be represented by this cartoon. Library(vcfR)data(vcfRexample)vcf ##. Object of Class vcfR.## 18 samples## 1 CHROMs## 2,533 variants## Object size: 3.2 Mb## 8.497 percent missing data##.The function library loads libraries, in this case the package vcfR. The function data loads datasets that were included with R and its packages.
Our usage of data loads the objects ‘gff’, ‘dna’ and ‘vcf’ from the ‘vcfRexample’ dataset. Here we’re only interested in the object ‘vcf’ which contains example VCF data. When we call the object name with no function it invokes the ‘show’ method which prints some summary information to the console. Strwrap(vcf @meta 1: 7) ## 1 '##fileformat=VCFv4.1'## 2 '##source='GATK haplotype Caller, phased with beagle4'## 3 '##FILTER='## 4 '##FORMAT='## 6 '##FORMAT='## 8 '##FORMAT='## 10 '##FORMAT='The first line contains the version of the VCF format used in the file. This line is required. The second line specifies the software which created the VCF file. This is not required, so not all VCF files include it.
When they do, the file becomes self documenting. Note that the alignment software is not included here because it was used upstream of the VCF file’s creation (aligners typically create.SAM or.BAM format files). Because the file can only include information about the software that created it, the entire pipeline does not get documented.
Some VCF files may contain a line for every chromosome (or supercontig or contig depending on your genome), so they may become rather long. Here, the remaining lines contain INFO and FORMAT specifications which define abbreviations used in the fix and gt portions of the file.The meta region may include long lines that may not be easy to view.
In vcfR we’ve created a function to help press this data. QueryMETA(vcf, element = 'DP') ## 1## 1 'FORMAT=ID=DP'## 2 'Number=1'## 3 'Type=Integer'## 4 'Description=Approximate read depth (reads with MQ=255 or with bad mates are filtered)'#### 2## 1 'INFO=ID=DP'## 2 'Number=1'## 3 'Type=Integer'## 4 'Description=Approximate read depth; some reads may have been filtered'When an element parameter is included, only the information about that element is returned. In this example the element ‘DP’ is returned. We see that this acronym is defined as both a ‘FORMAT’ and ‘INFO’ acronym. We can narrow down our query by including more information in the element parameter.
![Vcf Samples Correlation Vcf Samples Correlation](http://mutalisk.org/img/document/Picture16.png)
QueryMETA(vcf, element = 'FORMAT=. The fix regionThe fix region contains information for each variant which is sometimes summarized over all samples. The first eight columns of the fixed region are titled CHROM, POS, ID, REF, ALT, QUAL, FILTER and INFO. This is per variant information which is ‘fixed’, or the same, over all samples. The first two columns indicate the location of the variant by chromosome and position within that chromosome. Here, the ID field has not been used, so it consists of missing data (NA). The REF and ALT columns indicate the reference and alternate allelic states for a diploid sample.
When multiple alternate allelic states are present they are delimited with commas. The QUAL column attempts to summarize the quality of each variant over all samples.
The FILTER field is not used here but could contain information on whether a variant has passed some form of quality assessment. Head( getFIX(vcf)) ## CHROM POS ID REF ALT QUAL FILTER## 1, 'Supercontig1.50' '2' NA 'T' 'A' '44.44' NA## 2, 'Supercontig1.50' '246' NA 'C' 'G' '144.21' NA## 3, 'Supercontig1.50' '549' NA 'A' 'C' '68.49' NA## 4, 'Supercontig1.50' '668' NA 'G' 'C' '108.07' NA## 5, 'Supercontig1.50' '765' NA 'A' 'C' '92.78' NA## 6, 'Supercontig1.50' '780' NA 'G' 'T' '58.38' NAThe eigth column, titled INFO, is a semicolon delimited list of information. It can be rather long and cumbersome.
The function getFIX will suppress this column by default. Each abbreviation in the INFO column should be defined in the meta section. We can validate this by querying the meta portion, as we did in the ‘meta’ section above.
The gt regionThe gt (genotype) region contains information about each variant for each sample. The values for each variant and each sample are colon delimited. Multiple types of data for each genotype may be stored in this manner.
The format of the data is specified by the FORMAT column (column nine). Here we see that we have information for GT, AD, DP, GQ and PL. The definition of these acronyms can be referenced by querying the the meta region, as demonstrated previously. Every variant does not necessarily have the same information (e.g., SNPs and indels may be handled differently), so the rows are best treated independently. Different variant callers may include different information in this region.
Vcf @gt 1: 6, 1: 4 ## FORMAT BL2009P4us23## 1, 'GT:AD:DP:GQ:PL' '0 0:62,0:62:99:0,190,2835'## 2, 'GT:AD:DP:GQ:PL' '1 0:5,5:10:99:111,0,114'## 3, 'GT:AD:DP:GQ:PL' NA## 4, 'GT:AD:DP:GQ:PL' '0 0:1,0:1:3:0,3,44'## 5, 'GT:AD:DP:GQ:PL' '0 0:2,0:2:6:0,6,49'## 6, 'GT:AD:DP:GQ:PL' '0 0:2,0:2:6:0,6,49'## DDR7602 IN2009T1us22## 1, '0 0:12,0:12:39:0,39,585' '0 0:37,0:37:99:0,114,1709'## 2, NA '0 1:2,1:3:16:16,0,48'## 3, NA '0 0:2,0:2:6:0,6,51'## 4, NA '1 1:0,1:1:3:25,3,0'## 5, '0 0:1,0:1:3:0,3,34' '0 0:1,0:1:3:0,3,31'## 6, '0 0:1,0:1:3:0,3,34' '0 0:3,0:3:9:0,9,85'. Head(vcf) ## 1 '. Object of class 'vcfR'.' ## 1 '. Meta section.'
## 1 '##fileformat=VCFv4.1'## 1 '##source='GATK haplotype Caller, phased with beagle4'## 1 '##FILTER='## 1 '##FORMAT='## 1 'First 6 rows.'