Long-read hybrid CNV caller (LRHCNV)

LRHCNV utilises long-reads and short-reads to call structural variants.

The long reads are used to uncover a set of putative CNVs, and then the short reads are used to provide support for the extracted breakpoints.

Simplied version of the pipeline utilised a moleculo genome assembly is shown below.

Input file format for pilon running (tab or comma-delimited).

    SAMPLE_NAME SCAFFOLDS PE SE
    SM1 SM.fasta P1*.gz:P2*.gz,P1*.gz:P2*.gz fastq.gz