Was recently asked about HGVS nomenclature reporting. The fun thing about biology is that there's going to be exceptions to the rule or some shenanigans that you didn't expect when setting out a rule.  "The Human Genome Variation Society (HGVS) provides standardized recommendations for describing human sequence variants, which are widely accepted in the scientific community, especially in the practice of clinical molecular pathology.1 Use of the HGVS nomenclature system is a de facto recommendation for clinical reporting of sequence variants.2, 3 Being a core component of the clinic ..read more

 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   https://github.com/GoekeLab/bioinformatics-workflows     ..read more

 strand bias and orientation bias – GATK (broadinstitute.org) " 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 ..read more

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 callin ..read more

 Had to work with Ion Torrent BAMs for this but I think it's applicable to everything   Needed to run this on unmapped reads so running this first. After that the next script is fairly simple  Will share the install when I have time. A major hiccup for me was realising not all pre-built db works with Kraken2 ..read more

  This command allows you to see what apps are consuming internet. ss -p ..read more

 This software company did something that I didn't expect... putting the variant calling on the phone itself .. "The variant calling is run directly on the phone, extracting the data from the file on your phone, processed on the phone, and only at the end the VCF file could be shared in the cloud for annotation and reporting by an accredited physician," Ascari said. The physician is necessary to assure that the result is of "diagnostic quality," he added. I honestly expected CRAM & cloud based calling with encrypted exchange (made feasible with 5G mobile network) of bam reads with an ..read more

 Sharing a newly published article where a novel c.682‐2delA variant involving the AG consensus at the 3′ end of BRCA2 intron 8 was detected. The case involved a 33‐year‐old Italian breast cancer patient belonging to a HBOC family (BRCAPro score: 88%) with no other known pathogenic BRCA mutation.    A novel BRCA2 splice variant identified in a young woman - Nicolussi - - Molecular Genetics & Genomic Medicine ..read more

 I am intrigued that this Genome assembly guide includes mention of SOLID and Ion Torrent ... although not much information is given on how to work on them for genome assembly.  That said, perhaps the SPADES plugin provided with the sequencer solves most of everyone's immediate needs ... Wondering how improve on evaluating the assemblies  ..read more

 IonCRAM: a reference-based compression tool for ion torrent sequence files https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7487613/   IonCRAM, the first reference-based compression tool to compress Ion Torrent BAM files for long term archiving. For the BAM files, IonCRAM could achieve a space saving of about 43%. This space saving is superior to what achieved with the CRAM format by about 8–9%. Future research for reducing the space consumption of the Ion Torrent BAM files would include the binning of the flow signal and quality values. The idea of binning was initially introduced ..read more