PhaseDenovo

This repo includes the R script to phase de novo variant based on long and short-read sequencing data.

Input files

1. A bed file includes de novo variants:

• Chrom
• pos
• REF
• ALT

2. vcf file with variant phased using whatshap(v.1.0) run whatshap using short-read and long-read data to get the physical phased variant (0|1, 1|0, etc.)

[~]$ whatshap phase -o phased.vcf --reference=reference.fasta input.vcf nanopore.bam pacbio.cram illumina.bam

Run on Rstudio

Example of running the script in Rstudio.

Session infor