HapTree-X is a computational tool that phases various kinds of next-generation sequencing data. Currently, it supports whole-genome, whole-exome, 10X Genomics and RNA-seq data. It is especially powerful on RNA-seq data as it can utilize allelic imbalance to better phase genic regions.

HapTree-X binaries are available for Linux and macOS under releases.

To build HapTree-X from scratch, you will need the latest version of Seq compiler and llc (typically shipped with LLVM).

Then, issue make to build HapTree-X. The resulting binary will be located in build/haptreex.

Basic usage is:

haptreex -v [VCF file with variants to be phased]
         -d [indexed SAM, BAM or CRAM file with the aligned reads]
         -o [output file]

For RNA-seq data, use:

haptreex -v [VCF file with variants to be phased]
         -r [indexed SAM, BAM or CRAM file with the aligned reads]
         -g [GTF file compatible with the provided SAM/BAM/CRAM]
         -o [output file]

-g parameter is optional. However, its inclusion will result in better phases.

HapTree-X can also phase both DNA and RNA-seq samples at the same time. An example would be:

haptreex -v [VCF file with variants to be phased]
         -r [indexed RNA-seq SAM, BAM or CRAM file with the aligned reads]
         -d [indexed WGS/WXS SAM, BAM or CRAM file with the aligned reads]
         -g [GTF file compatible with the provided SAM/BAM/CRAM]
         -o [output file]

If you want to phase 10X genomics samples, pass --10x flag to HapTree-X.

Finally, HapTree-X can be run in multi-threaded mode. To enable it, set the OMP_NUM_THREADS variable to the desired number of threads. An example would be:

OMP_NUM_THREADS=4 haptreex -v ...

HapTree-X's output follows the HapCUT output format convention. The output file will contain the set of phased haplotype blocks in a list format where the beginning of each block starts with BLOCK and the end of each block is indicated by *****.

Each line in between contains 5 tab-delimited fields, which are in order:

1. Line number in the VCF file (ignoring header lines) that contain the het-SNP
2. Phase of the het-SNP corresponding to the first digit in 0|1 or 1|0
3. Phase of the het-SNP corresponding to the second digit in 0|1 or 1|0
4. Chromosome name
5. Chromosome position

Experimental notebook and the scripts used to generate the relevant paper data are located in paper/ directory.

For questions or issues, either open GitHub issue or contact us at:

• Ibrahim Numanagić (inumanag at uvic dot canada)
• Lillian Zhang (lillianz at mit dot education)