Compare GOR reports

This query compares variants in two variant reports. The output is a table with variant coordinates and a calculated column categorizing variants as follows:

• Present in only report 1 (R1)

• Present in only report 2 (R2)

• Present in both reports (R1,R2)

Compare GOR Reports module in Sequence Miner

Example use case

A user wishes to identify variants common to two possibly genetically-related phenotypes and runs the Multi-family Mendelian analysis report builder separately on two sets of cases:

• Cases with progressive vision loss

• Cases with progressive hearing loss

The user can run this report builder using each Multi-family Mendelian analysis report as input to identify variants common to both sets of cases and those unique to one set or the other.

Description of the algorithm

The algorithm creates a table listing the union of all variants in both reports (all variants in R1 and R2, one variant per row), and calculates a Source column in which each variant is denoted as belonging to the intersection of both reports (R1,R2) or belonging only to R1 or R2.

Interpreting the output

The user can choose to have the default display of the output in vertical or horizontal format:

• In the vertical format, there is a single PN column listing the index for the report in which the variant is present.

• In the horizontal format, each variant has an R1_PN column and an R2_PN column. Only one of these cells can be populated per row. Therefore, if a variant is present in both R1 and R2, then the variant is listed in two rows.

Column descriptions

Report output columns and descriptions

Group	Column	Description
Basic	Call	The actual called sequence (variant), found by replacing a part of the reference sequence, denoted by Pos and Reference, with the sequence in the Call column
	Chrom	The chromosome of the variant, represented as chr1, chr2, …, chr22, chrXY, chrX, chrY, chrM
	PN	The patient number (identifier)
	Pos	The (first) base pair position of the sequence variant, e.g., the position of the first nucleotide in the Reference column
	Reference	Sequence from the reference build, the first base starting at the base pair position in the Pos column
Other columns	CallCopies	Because the focus is only on variations from the reference, CallCopies refers to how many copies of the variation exist in the subject; “2” corresponds to a homozygous variation whereas “1” corresponds to a heterozygous variation
	CallRatio	Proportion of reads containing the variation call; expected to be close to 0.5 for heterozygous calls and close to 1 for homozygous calls
	Depth	The number of reads used in evaluating the corresponding call
	FILTER	Quality parameter using the ratio between gt-quality and depth showing if the call is considered of “LowQual” quality (not useable) or “PASS”; this is still a very crude quality measure
	formatZip	VCF genotype fields
	FS	Fisher’s exact test of read strand; if the reference reads are balanced between forward and reverse strands, then the alternate reads should be as well
	GL_Call	A statistical measure indicating the likelihood the call is wrong; the scale has been converted to use only integer numbers - the higher the number, the less likely it is that the call is wrong
	Source	Displays each source report ID; if multiple subjects or reports contain a variant, then the variant will be listed in multiple rows with one report ID per row (e.g., “R1” or “R2”)
	Sources	Displays the variant reports that contain this variant; if multiple reports contain this variant, the value will be a comma-delimited list (“R1,R2,…”)

Note

Annotation columns are derived from input files.

Perspective views

The Default view perspective shows all variants in either report with complete column annotations from source reports. Additional Perspectives focus on subsets of the columns in the default view.

Perspectives

Perspective	Description
Both	Variants in both reports with five columns: Chrom, POS, Reference, Call, Sources
Default view	Shows all variants in either report with complete column annotations from source reports
Either	Variants present in either report with five columns: Chrom, POS, Reference, Call, Sources
R1only	Variants uniquely found in R2 report with five columns: Chrom, POS, Reference, Call, Sources
R2only	Variants uniquely found in R2 report with five columns: Chrom, POS, Reference, Call, Sources