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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: <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 for support and questions.

Jessica Bene, Ashwini Bhasi, Chris Gates, Kevin Meng, Peter Ulintz - UM BRCF Bioinformatics Core

Project details

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