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code-110116.tar.gz
readme.md

readme.md

This directory contains code for FragmentCut, a method for the detection of long DNA fragments from dilution pool sequencing experiments.

Input for FragmentCut:

  1. sorted BAM file for each pool
  2. reference fasta file (indexed)
  3. genome mappability file (fasta format)
  4. VCF file with heterozygous variants

Output from FragmentCut:

  1. bedfile with list of fragment intervals
  2. HapCUT formatted fragment file for haplotype assembly