TY - JOUR T1 - SCReadCounts: Estimation of cell-level SNVs from scRNA-seq data JF - bioRxiv DO - 10.1101/2020.11.23.394569 SP - 2020.11.23.394569 AU - NM Prashant AU - Nawaf Alomran AU - Yu Chen AU - Hongyu Liu AU - Pavlos Bousounis AU - Mercedeh Movassagh AU - Nathan Edwards AU - Anelia Horvath Y1 - 2020/01/01 UR - http://biorxiv.org/content/early/2020/11/23/2020.11.23.394569.abstract N2 - SCReadCounts is a method for a cell-level estimation of the sequencing read counts bearing a particular nucleotide at genomic positions of interest from barcoded scRNA-seq alignments. SCReadCounts generates an array of outputs, including cell-SNV matrices with the absolute variant-harboring read counts, as well as cell-SNV matrices with expressed Variant Allele Fraction (VAFRNA); we demonstrate its application to estimate cell level expression of somatic mutations and RNA-editing on cancer datasets. SCReadCounts is benchmarked against GATK and Samtools and is freely available as a 64-bit self-contained binary distribution (Linux), along with MacOS and Python installation.Availability https://github.com/HorvathLab/NGS/tree/master/SCReadCountsSupplementary Information SCReadCounts_Supplementary_Data.zipCompeting Interest StatementThe authors have declared no competing interest. ER -