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https://github.com/0xTCG/haptreex
Haplotype phaser for next-generation sequencing data
https://github.com/0xTCG/haptreex
Last synced: 2 months ago
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Haplotype phaser for next-generation sequencing data
- Host: GitHub
- URL: https://github.com/0xTCG/haptreex
- Owner: 0xTCG
- License: agpl-3.0
- Created: 2018-10-23T02:09:11.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2022-01-13T17:34:33.000Z (almost 3 years ago)
- Last Synced: 2024-07-31T20:28:56.871Z (5 months ago)
- Language: Jupyter Notebook
- Homepage: https://haptreex.csail.mit.edu
- Size: 424 KB
- Stars: 13
- Watchers: 5
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
Awesome Lists containing this project
- awesome-linked-reads - HapTree-X - generation sequencing data| (Tools)
README
# HapTree-X
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.
## Installation
HapTree-X binaries are available for Linux and macOS under [releases](https://github.com/0xTCG/haptreex/releases).
## Building
To build HapTree-X from scratch, you will need the latest version of [Seq compiler](https://seq-lang.org) and [llc](https://llvm.org/docs/CommandGuide/llc.html) (typically shipped with LLVM).
Then, issue `make` to build HapTree-X. The resulting binary will be located in `build/haptreex`.
## Usage
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 ...
```
## Output
HapTree-X's output follows the [HapCUT](https://github.com/vibansal/HapCUT2) 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
## Paper data
Experimental notebook and the scripts used to generate the relevant paper data are located in [paper/](paper) directory.
## Contact
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)