The Pediatric Soft Tissue Sarcoma Paper, a COVID lock-down side quest and what is a genomic variant

Our paper Germline variants in patients diagnosed with pediatric soft tissue sarcoma. was published during the summer. This paper began with the story of a young male with a sarcoma in the prostate. This is a very rare condition. The treating physician wanted to find better treatment options and in an attempt to get some clues to what, our lab did 360 gene panel DNA sequencing to see if there was any targetable mutations that could direct the treatment of this young man.

Dragen QC report template for multiple samples from fastqc metrics

A Rmarkdown report generator for Dragen fastqc metrics

NGS sequencing file formats

Sequencing data comes in a wide variety of formats and they contain very specific information. This is a collection of notes on different formats, and how to interact with some of them using command line tools like samtools, or R. Next Generation Sequencing (NGS) technology in brief: NGS and Sanger sequencing is similar in principle. DNA polymerase adds fluorescent nucleotides to a growing DNA template strand. DNA bases are identified when each base C, T, G, A, emits a fluorescent signal as they are added to a nucleic acid chain.