A simple script for counting of a number of haplotypes formed by pre-selected SNPs in long-read sequencing data. The number of haplotypes is counted per 1kb in individual long sequencing reads aligned to a reference, based on the position, reference and alternative alleles of reliable SNPs called on short-read sequencing data Required input files: - processed long sequencing reads aligned to the reference and split per chromosome/contig into individual files - the names must correspond with the respective vcf files - vcf files with reliable biallelic SNPs split per chromosome/contig into individual files - the names must correspond with the respective bam files - file with names for each chromosome/contig - has to be the same as names for bam and vcf files Required software: - Java version 1.8 or higher - downloaded and compiled sam2tsv.jar from jvarkit https://github.com/lindenb/jvarkit

This work was supported by Erwin Schrödinger fellowship from Austrian Science Fund (FWF) (project number J3692-B22)