Daily Digest

Tumors are complex tissues of cancerous cells surrounded by a heterogeneous cellular microenvironment with which they interact. Here, researchers propose ikarus, a machine learning pipeline aimed at distinguishing tumor cells from normal cells at the single-cell level. Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies--as well as in somatic and germline mutation studies. Here the authors present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, they wrote and made available through the multiple vcflib, bio-vcf, cyvcf2, hts-nim and slivar projects. These tools are applied for comparison, filtering, normalisation, smoothing and annotation of VCF, as well as output of statistics, visualisation, and transformations of files variants.