Pisces

[] [Bioinformatics]

Pisces: An Accurate and Versatile Variant Caller for Somatic and Germline Next-Generation Sequencing Data

“a rapid, versatile and accurate small variant calling suite designed for somatic and germline amplicon sequencing applications. Accuracy is achieved by four distinct modules, each incorporating a number of novel algorithmic strategies.”

DeepVariant

[PMID: 30247488] [Nature Biotechnology]

A universal SNP and small-indel variant caller using deep neural networks

Google’s toy “a deep convolutional neural network can call genetic variation in aligned next-generation sequencing read data by learning statistical relationships between images of read pileups around putative variant and true genotype calls. ” “DeepVariant can learn to call variants in a variety of sequencing technologies and experimental designs, including deep whole genomes from 10X Genomics and Ion Ampliseq exomes”

Mutation Signature and Replication Timing

[PMID: 30201020] [Genome Biology]

Mutational signature distribution varies with DNA replication timing and strand asymmetry

“we use somatic mutation signatures—each representing a mutagenic process—derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions… We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. “