Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods

 Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods 

 

https://www.nature.com/articles/s41592-021-01254-9

Reproducible, scalable, and shareable analysis pipelines with bioinformatics workflow managers | Nature Methods The rapid growth of high-throughput technologies has transformed biomedical research. With the increasing amount and complexity of data, scalability and reproducibility have become essential not ... www.nature.com

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https://github.com/GoekeLab/bioinformatics-workflows    

GitHub - GoekeLab/bioinformatics-workflows: minimal example implementations for bioinformatics workflow managers Workflow managers provide an easy and intuitive way to simplify pipeline development. Here we provide basic proof-of-concept implementations for selected workflow managers. The analysis workflow is based on a small portion of an RNA-seq pipeline, using fastqc for quality controls and salmon for ... github.com

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Orientation Bias artifect

 strand bias and orientation bias – GATK (broadinstitute.org)

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The read orientation artifact, also known as the orientation bias artifact, arises due to a chemical change in the nucleotide during library prep that results in, for example, G base-paring with A. This kind of artifact has a clear signature (e.g. C to A SNP that occurs predominantly for the middle C in the DNA sequence CCG), and it’s singlestranded in nature. Downstream, this artifact manifests as low allele fraction SNPs whose evidence for the alt allele consists almost entirely F1R2 reads or F2R1 reads. A read pair is F1R2 (forward 1st, reverse 2nd) if the sequence of bases in Read 1 maps to the forward strand of the reference (F1), and the sequence of Read 2 to the reverse strand
of the reference (R2). F2R1 is defined similarly

 

if someone has read the dragonbioit used guide in illumina, it just mentioned orientation bias, ignore the strand bias.

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Benchmarking variants and comparing truth sets: List of useful tools and publications

Just realised that other than vcf-compare and bedtools intersect 

there's other options

 

https://github.com/RealTimeGenomics/rtg-tools

https://github.com/Illumina/hap.py

 

Also there's actually new variant callers ..

Molina-Mora, J.A., Solano-Vargas, M. Set-theory based benchmarking of three different variant callers for targeted sequencing. BMC Bioinformatics 22, 20 (2021). https://doi.org/10.1186/s12859-020-03926-3

 

Krishnan, V., Utiramerur, S., Ng, Z. et al. Benchmarking workflows to assess performance and suitability of germline variant calling pipelines in clinical diagnostic assays. BMC Bioinformatics 22, 85 (2021). https://doi.org/10.1186/s12859-020-03934-3

Additional file 23: File 3

. verify_variants.py

 

 

Zook, Justin M et al. “An open resource for accurately benchmarking small variant and reference calls.” Nature biotechnology vol. 37,5 (2019): 561-566. doi:10.1038/s41587-019-0074-6

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

hgvs.readthedocs.io/

• hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update.

  Wang M, Callenberg KM, Dalgleish R, Fedtsov A, Fox NK, Freeman PJ, Jacobs KB, Kaleta P, McMurry AJ, Prlić A, Rajaraman V, Hart RK.Hum Mutat. 2018 Dec;39(12):1803-1813. doi: 10.1002/humu.23615. Epub 2018 Sep 5.PMID: 30129167 Free PMC article.

  • Sequence Variant Descriptions: HGVS Nomenclature and Mutalyzer.

    den Dunnen JT.Curr Protoc Hum Genet. 2016 Jul 1;90:7.13.1-7.13.19. doi: 10.1002/cphg.2.PMID: 27367167

   

• A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature.

  Hart RK, Rico R, Hare E, Garcia J, Westbrook J, Fusaro VA.Bioinformatics. 2015 Jan 15;31(2):268-70. doi: 10.1093/bioinformatics/btu630. Epub 2014 Sep 30.PMID: 25273102 Free PMC article.
• VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions.

  Freeman PJ, Hart RK, Gretton LJ, Brookes AJ, Dalgleish R.Hum Mutat. 2018 Jan;39(1):61-68. doi: 10.1002/humu.23348. Epub 2017 Oct 17.PMID: 28967166 Free PMC article.
• Clinical Implementation and Validation of Automated Human Genome Variation Society (HGVS) Nomenclature System for Next-Generation Sequencing-Based Assays for Cancer.

  Callenberg KM, Santana-Santos L, Chen L, Ernst WL, De Moura MB, Nikiforov YE, Nikiforova MN, Roy S.J Mol Diagn. 2018 Sep;20(5):628-634. doi: 10.1016/j.jmoldx.2018.05.006. Epub 2018 Jun 21.PMID: 29936258