Science Score: 20.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: zenodo.org -
✓Committers with academic emails
8 of 15 committers (53.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (14.9%) to scientific vocabulary
Keywords
Repository
Tools for processing and analyzing structural variants.
Basic Info
Statistics
- Stars: 154
- Watchers: 17
- Forks: 56
- Open Issues: 73
- Releases: 0
Topics
Metadata Files
README.md
svtools - Comprehensive utilities to explore structural variations in genomes
Summary
svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls. It is designed to efficiently merge and genotype calls from speedseq sv across thousands to tens of thousands of genomes.
Table of Contents
Requirements
- A Linux-like environment with bash, awk, and sort
- A working installation of
cnvnator-multi(a component ofspeedseq sv) - Python2.7
- Numpy
- Scipy
- Pandas
- Statsmodels
- SVTyper (0.7.0)
Installation
We recommend you install using pip. For more detailed instructions, see our Installation guide.
Installing via pip
pip install svtools
Obtaining help
Please see the documentation on, or linked to, this page. For additional help or to report a bug, please open an issue in the svtools repository: https://github.com/hall-lab/svtools/issues
Usage
svtools consists of subcommands for processing VCF or BEDPE files of structural variants and one accessory script (create_coordinates).
``` usage: svtools [-h] [--version] [--support] subcommand ...
Comprehensive utilities to explore structural variation in genomes
optional arguments: -h, --help show this help message and exit --version show program's version number and exit --support information on obtaining support
subcommand description lsort sort N LUMPY VCF files into a single file lmerge merge LUMPY calls inside a single file from svtools lsort vcfpaste paste VCFs from multiple samples copynumber add copynumber information using cnvnator-multi genotype compute genotype of structural variants based on breakpoint depth afreq add allele frequency information to a VCF file bedpetobed12 convert a BEDPE file to BED12 format for viewing in IGV or the UCSC browser bedpetovcf convert a BEDPE file to VCF vcftobedpe convert a VCF file to a BEDPE file vcfsort sort a VCF file bedpesort sort a BEDPE file prune cluster and prune a BEDPE file by position based on allele frequency varlookup look for variants common between two BEDPE files classify reclassify DEL and DUP based on read depth information ```
Citing svtools
Until svtools is published, please cite using its DOI. Note that this link corresponds to the latest version. If you used an earlier version then your DOI may be different and you can find it on Zenodo.
Troubleshooting
As issues arise and common problems are identified, we will list them here.
Note: For additional information and usage refer to the Tutorial.md file.
Owner
- Name: Ira Hall lab
- Login: hall-lab
- Kind: organization
- Location: St. Louis, Missouri
- Website: http://genome.wustl.edu/people/groups/detail/hall-lab/
- Repositories: 34
- Profile: https://github.com/hall-lab
GitHub Events
Total
- Issues event: 2
- Watch event: 3
- Issue comment event: 2
- Fork event: 2
Last Year
- Issues event: 2
- Watch event: 3
- Issue comment event: 2
- Fork event: 2
Committers
Last synced: almost 3 years ago
All Time
- Total Commits: 763
- Total Committers: 15
- Avg Commits per committer: 50.867
- Development Distribution Score (DDS): 0.321
Top Committers
| Name | Commits | |
|---|---|---|
| Dave Larson | d****n@g****u | 518 |
| abelhj | a****j@g****m | 85 |
| Colby Chiang | c****e@v****u | 61 |
| apregier | a****r@g****u | 25 |
| AbhijitBadve | b****t@g****m | 19 |
| Allison Regier | a****r@w****u | 17 |
| Jim Eldred | j****d@g****u | 11 |
| David Morton | d****n@g****m | 9 |
| Dave Larson | d****n@w****u | 6 |
| hall-lab | i****l@v****u | 3 |
| AbhijitBadve | A****e@u****m | 3 |
| Brent Pedersen | b****e@g****m | 2 |
| Colby Chiang | c****e@s****e | 2 |
| Jeff Jasper | q****8@u****t | 1 |
| Danny Antaki | d****i@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 73
- Total pull requests: 39
- Average time to close issues: 8 months
- Average time to close pull requests: 12 days
- Total issue authors: 53
- Total pull request authors: 7
- Average comments per issue: 1.48
- Average comments per pull request: 1.46
- Merged pull requests: 32
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 2
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 2
- Pull request authors: 0
- Average comments per issue: 0.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- ernfrid (7)
- anoronh4 (3)
- pingxinxing (3)
- edg1983 (2)
- deepalivasoya (2)
- jasonbhn (2)
- jjfarrell (2)
- Jordi-V (2)
- genostack (2)
- yachenhu (2)
- brentp (2)
- gwct (2)
- sususy (2)
- mike-molnar (1)
- sulinq (1)
Pull Request Authors
- ernfrid (29)
- apregier (4)
- brentp (2)
- dantaki (1)
- jasonbhn (1)
- iainrb (1)
- whelena (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 2
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Total downloads:
- pypi 162 last-month
- Total docker downloads: 329
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Total dependent packages: 0
(may contain duplicates) -
Total dependent repositories: 3
(may contain duplicates) - Total versions: 16
- Total maintainers: 3
proxy.golang.org: github.com/hall-lab/svtools
- Documentation: https://pkg.go.dev/github.com/hall-lab/svtools#section-documentation
- License: mit
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Latest release: v0.5.1
published over 6 years ago
Rankings
pypi.org: svtools
Tools for processing and analyzing structural variants
- Homepage: https://github.com/hall-lab/svtools
- Documentation: https://svtools.readthedocs.io/
- License: MIT
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Latest release: 0.5.1
published over 6 years ago
Rankings
Dependencies
- crcmod *
- google-auth *
- google-cloud-storage *
- google-compute-engine *
- logzero *
- numpy *
- pandas ==0.19.2
- scipy *
- setuptools *
- statsmodels *
- svtyper ==0.7.1