WhatsHap
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
Features
Very accurate results (Martin et al., WhatsHap: fast and accurate read-based phasing)
Works well with Illumina, PacBio, Oxford Nanopore and other types of reads
It phases SNVs, indels and even “complex” variants (such as TCG → AGAA)
Pedigree phasing mode uses reads from related individuals (such as trios) to improve results and to reduce coverage requirements (Garg et al., Read-Based Phasing of Related Individuals).
WhatsHap is easy to install
It is easy to use: Pass in a VCF and one or more BAM files, get out a phased VCF. Supports multi-sample VCFs.
It produces standard-compliant VCF output by default
If desired, get output that is compatible with ReadBackedPhasing
Open Source (MIT license)
Documentation
Read the documentation online. Offline documentation is available in the doc/ subdirectory in the repository and in the downloaded tar distribution.
Issue tracker
Please do not hesitate to use our issue tracker for bug reports and feature requests.
2 maintainers
Release files for whatshap 2.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| whatshap-2.0.tar.gz | 5.4 MB | Details |
Built distributions (wheels)
| File | Reset | |||
|---|---|---|---|---|
| whatshap-2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.11 | CPython 3.11 | Linux glibc 2.17+ x86-64 | Details |
| whatshap-2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.10 | CPython 3.10 | Linux glibc 2.17+ x86-64 | Details |
| whatshap-2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.9 | CPython 3.9 | Linux glibc 2.17+ x86-64 | Details |
| whatshap-2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.8 | CPython 3.8 | Linux glibc 2.17+ x86-64 | Details |
| whatshap-2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl | CPython 3.7 | CPython 3.7 pymalloc | Linux glibc 2.17+ x86-64 | Details |
Total release size: 36.6 MB
Release files / whatshap-2.0.tar.gz
| Download URL | whatshap-2.0.tar.gz |
|---|---|
| Size | 5.4 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Release files / whatshap-2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | whatshap-2.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.2 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
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|
Release files / whatshap-2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | whatshap-2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.2 MB |
| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Release files / whatshap-2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | whatshap-2.0-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.3 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Release files / whatshap-2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | whatshap-2.0-cp38-cp38-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.3 MB |
| Tags | CPython 3.8 Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
Release files / whatshap-2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | whatshap-2.0-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 6.2 MB |
| Tags | CPython 3.7 CPython 3.7 pymalloc Linux glibc 2.17+ x86-64 |
|
SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.17
|
