Somatic Genomics

Export Plots

px
px
X

Download the raw data used to create the plots in this report below:

Note that additional data was saved in post-processing_report_data when this report was generated.


Choose Plots

If you use plots from MultiQC in a publication or presentation, please cite:

MultiQC: Summarize analysis results for multiple tools and samples in a single report
Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
Bioinformatics (2016)
doi: 10.1093/bioinformatics/btw354
PMID: 27312411

Save Page

You can download the current html file for future use by clicking on the button below.

Download

Somatic Genomics

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

Pipeline overview

Our OPĀ² 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@biscglobal.com

Report info

Generated on
2021-06-28, 15:57
Report
Post-processing Report
Experiment
3ea4e09e-6626-4fe8-866d-4a2db0e0ba34
Step
mapping
Wet Lab
whole_exome
Target BED
s3://op2-experiments-5b5d6147-94a0-4101-a021-2afbf58279d3/3ea4e09e-6626-4fe8-866d-4a2db0e0ba34/supporting_files/target.bed
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 NameChange rateTs/TvM VariantsVarsSNPIndelTs/Tv
FreeBayes_AA
18868
16819
1250
1.95
FreeBayes_AA_snpEff
159730
2.164
0.02
FreeBayes_BB
29006
25550
2021
2.08
FreeBayes_BB_snpEff
106020
2.165
0.03
Manta_AA.tumorSV
6
0
1
0.00
Manta_AA.tumorSV_snpEff
57025161
0.000
0.00
Manta_BB.diploidSV
2
0
0
0.00
Manta_BB.diploidSV_snpEff
70937528
0.000
0.00
Strelka_AA_variants
52221
51552
669
1.59
Strelka_AA_variants_snpEff
57998
1.666
0.05
Strelka_BB_variants
70201
69405
796
1.97
Strelka_BB_variants_snpEff
43137
1.993
0.07

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).

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.

loading..

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
loading..

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.

loading..

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.
loading..

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.

loading..

Bcftools

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.

Variant Substitution Types

loading..

Variant Quality

loading..

Indel Distribution

loading..

Variant depths

Read depth support distribution for called variants

loading..

VCFTools

VCFTools is a program for working with and reporting on VCF files.

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

loading..

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

loading..

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
21.04.1
opp-variant-calling-dna
1.0
samtools
1.11
snpeff
4.3t
strelka
2.9.10
vcftools
0.1.16
vep
99.2