Fig. 1
From: Completing a genomic characterisation of microscopic tumour samples with copy number
PicoCNV pipeline overview. A. Large fragments of tumour DNA are distributed into wells such that each genomic locus is covered by at most one fragment per well, before being sequenced. B. Co-local short reads within each well are combined to create reconstructed large fragments (RLFs). Calculating the RDR from the RLF depth counteracts variations in the Illumina short read sequencing depth between fragments. C. Nearby SNPs supported by overlapping sets of wells come from the same allele. Calculating the BAF from well counts for haplotype blocks counteracts variations in sequencing depth. D. The de-noised RDR and BAF data are used to call allele-specific copy number alterations