This repo includes the R script to phase de novo variant based on long and short-read sequencing data.
- A bed file includes de novo variants:
- Chrom
- pos
- REF
- ALT
- 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
Example of running the script in Rstudio.