Command-line tools to expedite analysis of Variant Call Format (VCF) files.
Project description
Suite of command-line tools to expedite analysis of exome variant data from multiple patients and multiple variant callers.
## Usage
jacquard <subcommand> [options] [arguments]
For help on a specific subcommand: jacquard-runner.py <subcommand> –help
- ## Subcommands
- translate Accepts a directory of VCF results (including VarScan high
confidence files). Creates a new directory of VCFs, adding Jacquard-specific FORMAT tags for each VCF record.
- filter_hc_somatic Accepts a directory of Jacquard-tagged VCF results
from one or more callers and creates a new directory of VCFs, where rows have been filtered to contain only positions that were called as high-confidence somatic in any VCF.
- merge Accepts a directory of VCFs and returns a single
merged VCF file.
- summarize Accepts a Jacquard-merged VCF file and creates a new VCF
file, adding summary fields/tags.
- expand Transforms VCF file into tab-separated text file
expanding INFO fields and FORMAT tags into distinct columns.
Email bfx-jacquard@umich.edu for support and questions.
Jessica Bene, Ashwini Bhasi, Chris Gates, Kevin Meng, Peter Ulintz - UM BRCF Bioinformatics Core
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