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Somatic Genomics

A Variant Calling pipeline, implemented in Nextflow and part of the Online Pipelines Platform (OPP).

Pipeline overview

Our OP² somatic genomics pipeline is a bioinformatics analysis workflow used for whole genome, whole-exome and targeted DNA sequencing data. It allows you to analyze your DNA sequencing data using this gold standard analysis pipeline. You get insights into the quality of your data, identify small to large nucleotide and structural variation and annotate with biological knowledge.

The workflow processes raw data from FastQ inputs, aligns the reads, calls variants and performs variant annotation. These results are made available to you via two interactive reports, and a data package with all essential intermediate files to perform more in-depth data analysis. The pre-processing workflow processes your raw sequence data until QC approved aligned data. Next, the post-processing workflow enables you to review the biological meaning of your data via data annotation.

See the pipeline page for a more detailed overview.

Do you have any question about these results? Just email us at helpdesk@excelra.com

Report info

Generated on: 2023-09-12, 20:31
Report: Post-processing Report
Experiment: 3743a669-d0e6-4028-b897-5cad4ca92678
Step: mapping
Wet Lab: whole_genome
Species: homo_sapiens
Reference Build: GRCh38
Nucleotides/s: 1000.0
Skip MarkDuplicates: False
Fastq trim: Fastq trim selected
Trim R1: 0 bp
Trim R2: 0 bp
Trim 3' R1: 0 bp
Trim 3' R2: 0 bp
NextSeq Trim: 0 bp
snpEff DB: GRCh38.86
VEP cache version: 99

General Statistics

Showing ¹²/₁₂ rows and ⁷/₈ columns.

Sample Name	Change rate	Ts/Tv	M Variants	Vars	SNP	Indel	Ts/Tv	MNP
FreeBayes_SRR10022836				1028961	914724	66472	1.82	45557
FreeBayes_SRR10022836_snpEff	2929	1.965	1.05
FreeBayes_SRR10022854				1586381	1390315	113358	2.00	75311
FreeBayes_SRR10022854_snpEff	1933	2.050	1.60
Manta_SRR10022836.tumorSV				1239	0	624	0.00	0
Manta_SRR10022836.tumorSV_snpEff	2496580	0.000	0.00
Manta_SRR10022854.diploidSV				192	0	96	0.00	0
Manta_SRR10022854.diploidSV_snpEff	15786679	0.000	0.00
Strelka_SRR10022836_variants				3141197	3122063	19134	1.50	0
Strelka_SRR10022836_variants_snpEff	982	1.563	3.14
Strelka_SRR10022854_variants				4012880	3984100	28780	1.90	0
Strelka_SRR10022854_variants_snpEff	768	1.920	4.02

Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

Sort	Group	Column	Description	ID	Scale
\|\|	SnpEff	Change rate	Change rate	`Change_rate`	None
\|\|	SnpEff	Ts/Tv	Transitions / Transversions ratio	`Ts_Tv_ratio`	None
\|\|	SnpEff	M Variants	Number of variants before filter (millions)	`Number_of_variants_before_filter`	None
\|\|	Bcftools Stats	Vars	Variations total	`number_of_records`	None
\|\|	Bcftools Stats	SNP	Variation SNPs	`number_of_SNPs`	None
\|\|	Bcftools Stats	Indel	Variation Insertions/Deletions	`number_of_indels`	None
\|\|	Bcftools Stats	Ts/Tv	Variant SNP transition / transversion ratio	`tstv`	None
\|\|	Bcftools Stats	MNP	Variation multinucleotide polymorphisms	`number_of_MNPs`	None

SnpEff

SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes). .DOI: 10.4161/fly.19695.

Variants by Genomic Region

The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

Variant Effects by Impact

The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

There are four levels of impacts predicted by SnpEff:

High: High impact (like stop codon)
Moderate: Middle impact (like same type of amino acid substitution)
Low: Low impact (ie silence mutation)
Modifier: No impact

Variants by Effect Types

The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

This plot shows the effect of variants with respect to the mRNA.

Variants by Functional Class

The stacked bar plot shows the effect of variants and the number of variants for each effect type.

This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

Silent: The amino acid does not change.
Missense: The amino acid is different.
Nonsense: The variant generates a stop codon.

Variant Qualities

The line plot shows the quantity as function of the variant quality score.

The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

Bcftools

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.DOI: 10.1093/gigascience/giab008.

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

Read depth support distribution for called variants

VCFTools

VCFTools is a program for working with and reporting on VCF files.DOI: 10.1093/bioinformatics/btr330.

TsTv by Count

Plot of TSTV-BY-COUNT - the transition to transversion ratio as a function of alternative allele count from the output of vcftools TsTv-by-count.

Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Alternative allele count is the number of alternative alleles at the site. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-count

TsTv by Qual

Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

Software Versions

Software versions are collected at run time from the software output.

bcftools: 1.11
freebayes: v1.3.2-dirty
manta: 1.6.0
nextflow: 22.10.7
opp-variant-calling-dna: 1.0
snpeff: 4.3t
strelka: 2.9.10
vcftools: 0.1.16

Somatic Genomics

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Somatic Genomics

A Variant Calling pipeline, implemented in Nextflow and part of the Online Pipelines Platform (OPP).

Pipeline overview

Report info

General Statistics

SnpEff

Variants by Genomic Region

Variant Effects by Impact

Variants by Effect Types

Variants by Functional Class

Variant Qualities

Bcftools

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

VCFTools

TsTv by Count

TsTv by Qual

Software Versions

Somatic Genomics

Actions

Export Plots

Choose Plots

Save Page

Somatic Genomics

A Variant Calling pipeline, implemented in Nextflow and part of the Online Pipelines Platform (OPP).

Pipeline overview

Report info

General Statistics

General Statistics: Columns

SnpEff

Variants by Genomic Region

Variant Effects by Impact

Variants by Effect Types

Variants by Functional Class

Variant Qualities

Bcftools

Variant Substitution Types

Variant Quality

Indel Distribution

Variant depths

VCFTools

TsTv by Count

TsTv by Qual

Software Versions