https://github.com/databiosphere/xvcfview
A WDL workflow to subset, subsample, and filter VCF files using bcftools.
https://github.com/databiosphere/xvcfview
Last synced: 9 months ago
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A WDL workflow to subset, subsample, and filter VCF files using bcftools.
- Host: GitHub
- URL: https://github.com/databiosphere/xvcfview
- Owner: DataBiosphere
- Created: 2021-07-14T19:27:56.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2022-04-04T23:59:44.000Z (almost 4 years ago)
- Last Synced: 2025-06-01T06:52:29.127Z (10 months ago)
- Language: Python
- Homepage:
- Size: 401 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
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README
# xvcfview
This workflow provides the full power of [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view) to subset, subsample, and filter VCF files.
## input
All input files are referenced with either gs:// or drs:// URIs.
| parameter | required | default | description |
| --------- | -------- | :---------: | ----------- |
| `input_vcf` | required | | Input VCF file. |
| `input_vcf_index` | optional | | VCF index file. If omitted, an index is created during execution. Instructions for creating index files are [here](http://samtools.github.io/bcftools/bcftools.html#index). |
| `samples` | optional | | File of samples to be included in the output VCF. There should one sample per line. Additional information is [here](http://samtools.github.io/bcftools/bcftools.html#common_options). |
| `regions` | optional | | File of regions to be included in the output VCF. The file should contain tab separated columns of chromosome (e.g. 'chr15'), start position, and optionally end position. Additional information is [here](http://samtools.github.io/bcftools/bcftools.html#common_options). |
| `view_options` | optional | `-Oz` | Additional parameters to pass to the [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view) command. If modified, `view_options` should typically include `-Oz` to produce a gzipped output VCF. |
| `filters` | optional | | Filter arguments to pass into [bcftools view](http://samtools.github.io/bcftools/bcftools.html#view). Filters will be applied in a separate, subsequent, call to `bcftools view`. |
| `output_filename` | optional | `output.vcf.gz` | Name of the output vcf file. |
| `cpu` | optional | `8` | Number of CPU cores. |
| `memory` | optional | `64` | Amount of RAM in GB |
| `preemptible` | optional | `0` | Whether to use preemptible instances, which are cheaper but my be revoked during execution. |