Raw read counts and phased SNP counts for every single cell in the sequencing datasets of the breast cancer patient S1 from "Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL"

This dataset contains the raw read counts and phased SNP counts for every single cell in the sequencing datasets of breast cancer patient S1 from “Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL” [Zaccaria & Raphael, 2020]. These data enable the full reproduction of all the results in the related manuscript for breast cancer patient S1. Specifically, the data are provided in two files for every dataset DAT of patient S1 with the following format:

1. DAT.raw_read_counts.bed.gz is a multi-cell BED file containing the raw read counts in the following fields:
   • CHROMOSOME: the name of a human chromosome
   • START: the starting genomic position of a genomic bin in the chromosome
   • END: the ending genomic position of the genomic bin in the chromosome
   • CELL: the cell barcode that uniquely identifies a cell
   • NORMAL: the raw read count for the specified bin from a matched-normal sample
   • COUNT: the raw read count for the specified bin in the specified cell
   • RDR: the estimated read-depth ratio for the specified bin in the specified cell
2. DAT.phased_snps_counts.pos.gz is a multi-cell POS file containing the phased SNP counts in the following fields:
   • CHROMOSOME: the name of a human chromosome
   • POS: the genomic position in the chromosome of a germline SNP
   • CELL: the cell barcode that uniquely identifies a cell
   • COUNT_HAPLOTYPE_A: the count of reads that cover the SNP and that belong to haplotype A in the specified cell
   • COUNT_HAPLOTYPE_B: the count of reads that cover the SNP and that belong to haplotype B in the specified cell

All the files have been compressed using standard gzip.