Output Files

Sample

Sentrix barcode and position of the sample.

Rank

Rank of a single star allele solution for a gene. The top solution based on quality score is ranked as 1 with the alternative solutions ranked lower.

Gene or Variant

The gene symbol, or gene symbol plus rsID for variants.

Type

‘Haplotype’ (star allele) or ‘Variant’ PGx calling type.

Solution

Star allele or variant solution. If diploid, variant solutions have the format of Allele1/Allele2.

Solution Long

Long format solution for star alleles. The field has the following format: Structural Variant Type: Underlying Star allele.

An example of a long solution is: Complete: CYP2D64, Complete: CYP2D610, CYP2D668: CYP2D64 where there are two complete alleles that have CYP2D64 and CYP2D610 haplotypes and one CYP2D668 structural variant that has a CYP2D64 haplotype configuration.

Supporting Variants

All variants present in the array that support the star allele solution. The field has the following format: Long Solution Star Allele: (Supporting Variants).

Each supporting variant is listed with essential information extracted from the SNV VCF to assist with troubleshooting, including Chromosome, Location, Reference allele, Alternative allele, Genotype, GenCall score (GS), and B-allele frequency (BAF).

Missing/Masked Core Variants

All variants not present in the array or not called in the SNV VCF file for the star allele. The field has the following format: Long Solution Star-Allele: (Missing Variants).

All Missing Variants in Array

All core definition variants that are not on the array or are not called in the SNV VCF along with the associated star alleles that are impacted. The field has the following format: Missing Variant: (List of impacted star alleles).

Collapsed Star-Alleles

Star alleles that cannot be distinguished from the solution star allele given the input array’s content. The field has the following format: Long Solution Star-Allele: (List of collapsed star alleles).

The most frequent star allele based on the population frequency of PGx alleles will be the star allele in the solution.

Score

Quality score of the solution including the population frequency of PGx alleles. The score ranges from 0 to 1.

Raw Score:

Raw quality score of the solution without including the population frequency of PGx alleles. The score ranges from 0 to 1.

Copy Number Solution

Estimated copy number for each gene region. The field has the following format: Gene Region: Copy Number.

SNP Name

SNP identifier.

SNP

SNP alleles as reported by assay probes. Alleles on the Design strand (the ILMN strand) are listed in order of Allele A/B.

Sample ID

Sample identifier.

Allele 1 – Top

Allele 1 corresponds to Allele A and are reported on the Top strand.

Allele 2 – Top

Allele 2 corresponds to Allele B and are reported on the Top strand.

Allele 1 – Forward

Allele 1 corresponds to Allele A and are reported on the Forward strand.

Allele 2 – Forward

Allele 2 corresponds to Allele B and are reported on the Forward strand.

Allele 1 – Plus

Allele 1 corresponds to Allele A and are reported on the Plus strand.

Allele 2 – Plus

Allele 2 corresponds to Allele B and are reported on the Plus strand.

GC Score

Quality metric calculated for each genotype (data point), and ranges from 0 to 1.

GT Score

The SNP cluster quality. Score for a SNP from the GenTrain clustering algorithm.

Log R Ratio

Base-2 log of the normalized R value over the expected R value for the theta value (interpolated from the R-values of the clusters). For loci categorized as intensity only; the value is adjusted so that the expected R value is the mean of the cluster.

B Allele Freq

B allele frequency for this sample as interpolated from known B allele frequencies of 3 canonical clusters: 0, 0.5 and 1 if it is equal to or greater than the theta mean of the BB cluster. B Allele Freq is between 0 and 1, or set to NaN for loci categorized as intensity only.

Chr

Chromosome containing the SNP.

Position

SNP chromosomal position.

Locus_Name

Locus name from the manifest file.

Illumicode_Name

Locus ID from the manifest file.

#No_Calls

Number of loci with GenCall scores below the call region threshold.

#Calls

Number of loci with GenCall scores above the call region threshold.

Call_Freq

Call frequency or call rate calculated as follows: #Calls/(#No_Calls + #Calls)

A/A_Freq

Frequency of homozygote allele A calls.

A/B_Freq

Frequency of heterozygote calls.

B/B_Freq

Frequency of homozygote allele B calls.

Minor_Freq

Frequency of the minor allele.

Gentrain_Score

Quality score for samples clustered for this locus.

50%_GC_Score

50th percentile GenCall score for all samples.

10%_GC_Score

10th percentile GenCall score for all samples.

Het_Excess_Freq

Heterozygote excess frequency, calculated as (Observed -Expected)/Expected for the heterozygote class. If $f_{ab}$ is the heterozygote frequency observed at a locus, and p and q are the major and minor allele frequencies, then het excess calculation is the following: $(f_{ab} - 2pq)/(2pq + \varepsilon)$

ChiTest_P100

Hardy-Weinberg p-value estimate calculated using genotype frequency. The value is calculated with 1 degree of freedom and is normalized to 100 individuals.

Cluster_Sep

Cluster separation score.

AA_T_Mean

Normalized theta angles mean for the AA genotype.

AA_T_Std

Normalized theta angles standard deviation for the AA genotype.

AB_T_Mean

Normalized theta angles mean for the AB genotype.

AB_T_Std

Standard deviation of the normalized theta angles for the AB genotype.

BB_T_Mean

Normalized theta angles mean for the BB genotypes.

BB_T_Std

Standard deviation of the normalized theta angles for the BB genotypes.

AA_R_Mean

Normalized R value mean for the AA genotypes.

AA_R_Std

Standard deviation of the normalized R value for the AA genotypes.

AB_R_Mean

Normalized R value mean for the AB genotypes.

AB_R_Std

Standard deviation of the normalized R value for the AB genotypes.

BB_R_Mean

Normalized R value mean for the BB genotypes.

BB_R_Std

Standard deviation of the normalized R value for the BB genotypes.

Plus/Minus Strand

Designated "+" or "-" with respect to the reference genome strand. "U" designates unknown.

Failed to normalize and gencall sample: {sample_id}, it will be skipped. Error: The given key '{loci_id}' was not present in the dictionary.

Warning

This generally occurs because of a mismatch between the manifest (bpm) and cluster file (egt) (i.e., the cluster file was generated via a different manifest). To remedy the issue, use the manifest and cluster files intended for use together.

Reference allele is not queried for locus: {identifier}

Warning

True reference allele does not match any alleles in the manifest. The error is common for MNVs and will be addressed in future versions of the software.

Skipping non-mapped locus: {identifier}

Warning

Locus has no chromosome position (usually 0) These loci may be used for quality purposes or CNV calling only.

Skipping intensity only locus: {identifier}

Warning

Similar to non-mapped loci, intensity only probes have applications outside creating variants for SNV VCFs such as CNV calling.

Skipping indel: {identifier}

Warning

Indel context (deletion/insertion) could not be determined.

Failed to process entry for record: {identifier}

Warning

Unable to determine reference allele for indel.

Incomplete match of source sequence to genome for indel: {identifier}

Warning

Indel not properly mapped to the reference genome.

Failed to combine genotypes due to ambiguity - exm1068284 (InfiniumII): TT, ilmnseq_rs1131690890_mnv (InfiniumII): AA, rs1131690890_mnv (InfiniumII): AA

Warning

Detailed information about a NoCall ("./.”) in the VCF as a result of combining multiple probes that assay the same variant with conflicting results. The example here is two probes with homozygous REF genotypes (AA) and one probe with homozygous ALT probe (TT)

Cluster file ({GTC.egt}) is not the same as CN Model Cluster file ({CN_Model.egt}).

Warning

Cluster file used to generated GTCs used for copy number calling is not the same as was used for the GTCs used during copy number training that created the input CN model. Though CNV model is robust to minor cluster file updates, CNV training should be considered when there are significant updates in the cluster file. To remove the warning, copy number training needs to be re-run with the new GTCs generated via the new cluster file during genotyping, a different CN model with the expected cluster file needs to be used, or different GTCs should be used for copy number calling that were generated using the same cluster file as was used during the generation of the input CN model.

{numPassingSamples} sample(s) passed QC.

Requires at least {minPassingSamples} samples to proceed.

Error

CNV calling is batch dependent and requires a certain number of samples with high-quality to make accurate calls. More high-quality samples need to be added to analysis batch to resolve error.

Invalid manifest file path {manifestPath}

Error

Application could not find manifest file provided or user error.

Failed to load cluster file: {e.Message}

Error

Corrupted file or unsupported version.

softwareVersion

DRAGEN Array software version, e.g. dragena 1.0.0.

genomeBuild

Genome build, e.g hg38.

starAlleleDatabaseSources

Public databases with versions used as the sources of the star allele definitions and population frequencies.

phenotypeDatabaseSources

Public databases with versions used as the sources of the star allele phenotypes.

mappingFile

The PGx database file used for the star allele calling.

pgxGuideline

The PGx guidelines used for metabolizer status/phenotype annotations, e.g. CPIC or DPWG

sampleId

Sentrix barcode and position of the sample.

locusAnnotations

The star allele call information.

gene

The gene symbol.

callType

‘Star Allele’ or ‘Variant’ PGx calling type.

genotype

Most likely star allele or variant solution. If diploid, variant solutions have the format of Allele1/Allele2.

activityScore

Activity score annotation of the determined genotype of the gene determined based on public PGx guidelines CPIC or DPWG.

phenotypeDatabaseAnnotation

Metabolizer status and function annotations of the determined genotype of the gene based on lookup into public PGx guidelines CPIC or DPWG per user choice.

qualityScore

Quality score of the solution including the population frequency of PGx alleles. The score ranges from 0 to 1.

rawScore

Raw quality score of the solution without including the population frequency of PGx alleles. The score ranges from 0 to 1.

supportingVariants

All variants present in the array that support the star allele solution. The field provides an array (list) of supporting Variants.

Each supporting variant is listed with essential information extracted from the SNV VCF to assist with troubleshooting, including Chromosome (chrom), Location (pos), Reference allele (ref), Alternative allele (alt), Genotype (gt), GenCall score (gs), B-allele frequency (baf), the variant ID (id), and the associated star allele IDs (alleleIds).

candidateSolutions

The set of alternative star allele calling solutions, this is only relevant for genes of the ‘Star Allele’ call type.

missingVariantSites

All core variants that are not available (e.g. not on the array, or no calls in the SNV VCF) for star allele calling for this gene. For star alleles, the field provides an array (list) of variant "id" and impacted "alleleIds" pairs

allelesTested

Alleles that are covered by the star allele caller. The capability to call star alleles is also dependent on array content coverage and data quality. This field is defined by the array's content and will be the same across all samples.

rank

Rank of a single star allele solution for a gene. The top solution based on quality score is ranked as 1 with the alternative solutions ranked lower.

genotype

Star allele or variant solution. If diploid, variant solutions have the format of Allele1/Allele2.

activityScore

Activity score annotation of the determined genotype of the gene determined based on public PGx guidelines CPIC or DPWG.

phenotype

Metabolizer status and function annotations of the determined genotype of the gene based on lookup into public PGx guidelines CPIC or DPWG per user choice.

qualityScore

Quality score of the solution including the population frequency of PGx alleles. The score ranges from 0 to 1.

rawScore

Raw quality score of the solution without including the population frequency of PGx alleles. The score ranges from 0 to 1.

alleles

The composite alleles of the candidate genotype solution.

solutionLong

Long format solution for star alleles. The field has the following format: Structural Variant Type: Underlying Star allele.

An example of a long solution is: Complete: CYP2D64, Complete: CYP2D610, CYP2D668: CYP2D64 where there are two complete alleles that have CYP2D64 and CYP2D610 haplotypes and one CYP2D668 structural variant that has a CYP2D64 haplotype configuration.

supportingVariants

All variants present in the array that support the star allele solution. The field provides an array (list) of supporting Variants.

Each supporting variant is listed with essential information extracted from the SNV VCF to assist with troubleshooting, including Chromosome (chrom), Location (pos), Reference allele (ref), Alternative allele (alt), Genotype (gt), GenCall score (gs), B-allele frequency (baf), and the variant ID (id).

missingVariantSites

All variants not present in the array or not called in the SNV VCF file for the star allele solution. The field provides an array (list) of missing variants.

collapsedAlleles

Star alleles that cannot be distinguished from the solution star allele given the input array’s content. The field has the following format: Long Solution Star-Allele: (List of collapsed star alleles).

The most frequent star allele based on the population frequency of PGx alleles will be the star allele in the solution.

copyNumberRegions

Gene regions for the copy numbers listed in CopyNumberSolution.

copyNumberSolution

Estimated copy number for each gene region listed in CopyNumberRegions

Sentrix_ID

12-digit BeadChip Barcode associated with the sample.

Sentrix_Position

Row and column on the BeadChip ie R01C01

Sample_ID

Optional field that can be indicated using IDAT Sample Sheet

User Defined Meta Data

Optional field(s) that can be indicated using IDAT Sample Sheet. Any number of fields indicated will appear in this output file.

restoration

• The default threshold is 0.

• If using the FFPE DNA Restore Kit, the restoration control identifies success of the FFPE restoration chemistry. Change the threshold from 0 to 1 if the FFPE DNA Restore Kit was used.

• The green channel intensity is higher than Background. Therefore, the metric provided is the Green Channel Intensity/Background.

staining_green

staining_red

• Staining controls are used to examine the efficiency of the staining step in both the red and green channels. These controls are independent of the hybridization and extension step.

• The green channel shows a higher signal for biotin staining when compared to biotin background, whereas the red channel shows higher signal for DNP staining when compared to DNP background.

• The metric provided for green is the (Biotin High value)/ (Biotin Bkg) and the metric provided for red is (DNP High value)/(DNP Bkg value)

• The default threshold is 5. This threshold can be increased on some scanners.

extension_green

extension_red

• Extension controls test the extension efficiency of A, T, C, and G nucleotides from a hairpin probe, and are therefore sample independent.

• In the green channel, the lowest intensity for C or G is always greater than the highest intensity for A or T.

• The metric provided is the (lowest of the C or G intensity)/ (highest of A or T extension) for a single sample.

• The default threshold is 5. This threshold can be increased on some scanners.

hybridization_high_medium

hybridization_medium_low

• Hybridization controls test the overall performance of the Infinium Assay using synthetic targets instead of amplified DNA. These synthetic targets complement the sequence on the array, allowing the probe to extend on the synthetic target as a template. Synthetic targets are present in the Hybridization Buffer at 3 levels, monitoring the response from high-concentration (5 pM), medium concentration (1 pM), and low concentration (0.2 pM) targets. All bead type IDs result in signals with various intensities, corresponding to the concentrations of the initial synthetic targets.

• The value for high concentration is always higher than medium and the value for medium concentration is always higher than low.

• The metric provided is the value of high/medium and the value of medium/low.

• The default thresholds are 1. Do not change the default threshold.

target_removal1

target_removal2

• Target removal controls test the efficiency of the stripping step after the extension reaction. In contrast to allele-specific extension, the control oligos are extended using the probe sequence as a template. This process generates labeled targets. The probe sequences are designed such that extension from the probe does not occur. All target removal controls result in low signal compared to the hybridization controls, indicating that the targets were removed efficiently after extension. Target removal controls are present in the Hybridization Buffer.

• The Background for the same sample is close to or larger than either control.

• The metric provided is Background/Control Intensity.

• The default threshold is 1. Do not change the default threshold; however, the offset correction can be changed.

bisulfite_conversion1_green

bisulfite_conversion1_background_green

bisulfite_conversion1_red

bisulfite_conversion1_background_red

• These controls assess the efficiency of bisulfite conversion of the genomic DNA. The Infinium Methylation probes query a [C/T] polymorphism created by bisulfite conversion of non-CpG cytosines in the genome.

• These controls use Infinium I probe design and allele-specific single base extension to monitor efficiency of bisulfite conversion. If the bisulfite conversion reaction was successful, the "C" (Converted) probes matches the converted sequence and get extended. If the sample has unconverted DNA, the "U" (Unconverted) probes get extended. There are no underlying C bases in the primer landing sites, except for the query site itself.

• The calculation is done in both the green and red channels separately to provide 2 unique sets of values:

  • Green Channel

    • Lowest value of C1 or C2 / Highest value of U1 or U2. The default threshold is 1. This value can be increased for some scanners.

    • Background/(U1, or U2). The default threshold is 1. Do not change the default threshold; however, the offset correction can be changed.

  • Red Channel

    • Lowest value of C3, 4, or 5 / Highest value of U3, 4, or 5. The default threshold is 1. This value can be increased for some scanners.

    • Background /(Highest value of U4, U5, or U6). The default threshold is 1. Do not change the default threshold; however, the offset correction can be changed.

bisulfite_conversion2

bisulfite_conversion2_background

• These controls assess the efficiency of bisulfite conversion of the genomic DNA. The Infinium Methylation probes query a [C/T] polymorphism created by bisulfite conversion of non-CpG cytosines in the genome.

• These controls use Infinium II probe design and single base extension to monitor efficiency of bisulfite conversion. If the bisulfite conversion reaction was successful, the "A" base gets incorporated and the probe has intensity in the red channel. If the sample has unconverted DNA, the "G" base gets incorporated across the unconverted cytosine, and the probe has elevated signal in the green channel.

• The calculation is done using both channels for 1 set of numbers returned.

• The following metrics are provided:

  • (Lowest of red C 1, 2, 3, or 4) / (Highest of green C 1, 2, 3, or 4). The default threshold is 1. This value can be increased for some scanners.

  • Background/(Highest C1, C2, C3, or C4 green). The default threshold is 1. Do not change the default threshold; however, the offset correction can be changed.

specificity1_green

specificity1_red

• Specificity controls are designed to monitor potential nonspecific primer extension for Infinium I and Infinium II assay probes. Specificity controls are designed against nonpolymorphic T sites.

• These controls are designed to monitor allele-specific extension for Infinium I probes. The methylation status of a particular cytosine is carried out following bisulfite treatment of DNA by using query probes for unmethylated and methylated state of each CpG locus. In assay oligo design, the A/T match corresponds to the unmethylated status of the interrogated C, and G/C match corresponds to the methylated status of C. G/T mismatch controls check for nonspecific detection of methylation signal over unmethylated background. PM controls correspond to A/T perfect match and give high signal. MM controls correspond to G/T mismatch and give low signal.

• The metrics provided are the ratio of the lowest PM/highest MM in each channel.

• The default threshold is 1. Do not change the default threshold.

specificity2

specificity2_background

• Specificity controls are designed to monitor potential nonspecific primer extension for Infinium I and Infinium II assay probes. Specificity controls are designed against nonpolymorphic T sites.

• These controls are designed to monitor extension specificity for Infinium II probes and check for potential nonspecific detection of methylation signal over unmethylated background. Specificity II probes incorporate the "A" base across the nonpolymorphic T and have intensity in the Red channel. If there was nonspecific incorporation of the "G" base, the probe has elevated signal in the Green channel.

• The following metrics are provided:

  • (Lowest intensity of S1, S2, or S3 red) / (Highest intensity of S1, S2, or S3 green). The default threshold is 1. Do not change the default threshold.

  • Background/(Highest intensity S1, S2, S3, or S4 green). The default threshold is 1. Do not change the default threshold; however, the offset correction can be changed.

nonpolymorphic_green

nonpolymorphic_red

• Nonpolymorphic controls test the overall performance of the assay, from amplification to detection, by querying a particular base in a nonpolymorphic region of the genome. They let you compare assay performance across different samples. One nonpolymorphic control has been designed for each of the 4 nucleotides (A, T, C, and G).

• In the green channel, the lowest intensity of C or G is always greater than the highest intensity of A or T.

• The metric provided is the (lowest intensity for C or G) /(highest intensity for A or T) for a single sample.

• The default threshold is 5. This value can be increased for some scanners.

avg_green_raw

avg_red_raw

• Average green and red raw signal for the given sample.

avg_green_norm

avg_red_norm

• Average green and red signal after dye bias correction and noob normalization for the given sample.

ScanTime

• The date (MM/DD/YY) and time (HH:MM) that the sample was scanned by the iScan system.

NProbes

• Number of probes on the BeadChip, including SNP and CG probes

NPassDetection

• Number of probes on the BeadChip that passed detection p-value at the threshold defined.

prop_probes_passing

• The proportion of probes passing defined as the number of probes passing detection p-value divided by the total number of probes on the BeadChip.

passQC

• 1 = sample passed all QC metrics for the thresholds defined

• 0 = sample did not pass all QC metrics for the thresholds defined

failCodes

• The list of parameters that failed QC for the thresholds defined.

Control

Calculation

Additional Information

Restoration Green > bkg

(Green/(bkg+x))> 0

• If using the FFPE Restore kit, change the default threshold from 0 to 1.

• bkg = Extension Green highest A or T intensity

Staining Green

Biotin High > Biotin Bkg

(High/Biotin Bkg) > 5

Staining Red

DNP High > DNP Bkg

(High/DNP Bkg) > 5

Extension Green Lowest CG/Highest AT

(C or G/A or T) > 5

Green channel—Lowest C or G intensity is used; highest A or T intensity is used.

Extension Red

Lowest AT/Highest CG

(A or T/C or G) > 5

Red channel—Lowest A or T intensity is used; highest C or G intensity is used.

Hybridization Green High > Medium > Low

(High/Med) > 1 (Med/Low) > 1

Target Removal Green ctrl 1 ≤ bkg

((bkg + x)/ctrl) > 1

bkg = Extension Green highest A or T intensity

Target Removal Green ctrl 2 ≤ bkg

((bkg + x)/ctrl) > 1

bkg = Extension Green highest A or T intensity

Bisulfite Conversion I Green

C1, 2 > U1, 2

(C/U) > 1

• Lowest C intensity is used. Highest U intensity is used.

Bisulfite Conversion I Green

U ≤ bkg

((bkg + x)/U) > 1

• For MSA arrays, the default is 0.5

• Highest U intensity is used.

• Green channel—bkg = Extension Green highest AT

Bisulfite Conversion I Red C3, 4, 5 > U3, 4, 5

(C/U) >1

• Lowest C intensity is used. Highest U intensity is used.

Bisulfite Conversion I Red U ≤ bkg

((bkg + x)/U) > 1

• For MSA arrays, the default is 0.5

• Highest U intensity is used.

• Red Channel—bkg = Extension Red highest CG

Bisulfite Conversion II C Red > C Green

(C Red/ C Green) > 1

• For MSA arrays, the default is 0.5

• Lowest C Red intensity is used. Highest C Green intensity is used.

Bisulfite Conversion II C green ≤ bkg

((bkg + x)/C Green) > 1

• For MSA arrays, the default is 0.5

• Highest C Green intensity is used.

• Green channel—bkg = Extension Green highest AT

Specificity I Green PM > MM

(PM/MM) > 1

• Lowest PM intensity is used. Highest MM intensity is used

Specificity I Red PM > MM

(PM/MM) > 1

• Lowest PM intensity is used. Highest MM intensity is used

Specificity II

S Red > S Green

(S Red/ S Green) > 1

• Lowest S Red intensity is used. Highest S Green intensity is used.

Specificity II

S Green ≤ bkg

((bkg + x)/ S green) > 1

• bkg = Extension Green highest A or T intensity

• Highest S Green intensity is used.

Nonpolymorphic Green Lowest CG/ Highest AT

(C or G/ A or T) > 5

• Lowest C or G intensity is used; highest A or T intensity is used

• For MSA arrays, the default threshold is 2.5

Nonpolymorphic Red Lowest AT/ Highest CG

(A or T/ C or G) >5

• Lowest A or T intensity is used; highest C or G intensity is used

• For MSA arrays, the default threshold is 3

Proportion of Probes Passing Threshold

Histogram of the proportion of probes passing the p-value detection threshold. Samples passing QC are shown in one color, and samples failing QC are shown in another color.

Principal Component Analysis (PCA)

Uses beta values for all analytical probes to compare samples. Principal component analysis (PCA) is applied to the beta values to reduce the dimensionality of the data to two “principal components” that reflect the most variation across samples. If more than 100 samples are used in the analysis, a random subset of 10,000 probes are used for the PCA analysis to reduce computational burden. PCA control plot assigns unique colors to each sample group defined by the IDAT Sample Sheet. If no groups were assigned, all samples will appear the same color. Sample groups may cluster together and can be used to explain some of the variation. Coordinates used to plot each sample in the PCA control plot are provided in the pcs.tsv.gz output file (see below).

blank

BeadChip Barcode and Position ie 123456789101_R01C01

principal component 1

The variable of the first axis for the Principal Component Analysis

principal component 2

The variable of the second axis for the Principal Component Analysis

Sample_Group

Sample group defined by the user in the IDAT Sample Sheet. If no sample group was defined, all samples will show NA.

Probe_ID

This is a unique identifier for each probe. It corresponds to the IlmnID column in the standard Illumina manifest format or ctl_[AddressA_ID] for control probes.

U

This is corresponds to the AddressA_ID column in the standard Illumina manifest format.

M

This corresponds to the AddressB_ID column in the standard Illumina manifest format.

col

This is the color channel for Infinium I probes (R/G). For Infinium I probes, this column will be NA.

Address

The address of the probe

Type

The control probe type

Color_Channel

A color used to denote certain control probes in legacy software

Name

A human readable identifier for certain control probes

Probe_ID

This is a unique identifier for each probe. It corresponds to the IlmnID column in the standard Illumina manifest format or ctl_[AddressA_ID] for control probes.

Log

Error

Type

Cause

write_samplesheet.log

No IDATs found

Error

No IDATs provided for analysis

format_samplesheet.log

No samples in sample sheet

Error

No samples in user’s sample sheet input

format_samplesheet.log

Sample sheet not correctly formatted

Error

Sample sheet is not in CSV format or header lines do not start with “<”

format_samplesheet.log

beadChipName and sampleSectionName columns are required for the sample sheet.

Error

Sample sheet does not contain required columns: beadChipName and sampleSectionName.

format_samplesheet.log

Warning: <Number> samples have duplicate Sample_ID

Warning

X lines in the sample sheet have duplicate <beadChipName>_<sampleSectionName>. Duplicates are dropped from analysis.

convert_manifest_ilmn_sesame.log

Missing control probes in manifest

Error

Missing “[Controls]” line in CSV manifest

convert_manifest_ilmn_sesame.log

Probe section not found

Error

Missing “[Assay]” line in CSV manifest

convert_manifest_ilmn_sesame.log

Missing required columns: IlmnID, AddressA_ID, AddressB_ID, Color_Channel

Error

Missing one of required columns in Assay section of manifest

convert_manifest_ilmn_sesame.log

Controls not formatted correctly. Must have 4 columns (Address,Type,Color_Channel,Name)

Error

Missing one of required columns in Control section of manifest

run_sesame_gs.log

Missing sample: <Sample_ID>

Error

Missing idats for a particular sample

run_sesame_gs.log

No scan time available

Warning

No scan time in idat

run_sesame_gs.log

Prep failed

Error

Dye bias correction or noob failure for sample

run_sesame_gs.log

Warning: missing control probe types <Missing probes>

Warning

Missing control probe types to compute a BACR metric. Metric will be set to NA.

run_sesame_gs.log

Warning: missing control probe names <Missing probe types>

Warning

Missing control probes to compute a BACR metric. Metric will be set to NA.

qc.log

No features, skipping PCA plot

Warning

No common betas found in all samples. This may occur if a sample has no signal intensity in the IDAT files.