https://github.com/weinstockj/pileup_region

A simple rust application to count alt reads in a specified list of positions.
https://github.com/weinstockj/pileup_region

Last synced: about 1 month ago
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A simple rust application to count alt reads in a specified list of positions.

• Host: GitHub
• URL: https://github.com/weinstockj/pileup_region
• Owner: weinstockj
• License: gpl-3.0
• Created: 2020-07-31T20:30:33.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2023-12-11T16:06:35.000Z (about 1 year ago)
• Last Synced: 2024-04-24T03:15:04.420Z (8 months ago)
• Language: Rust
• Size: 16.6 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE.md

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README

        
## Pileup region

This is a simple rust application for counting the number of alt-reads and depths at locations

provided in a 1-based region file. It works for CRAM and BAMs. This has not been tested extensively. 

This application was developed to call U2AF1 mutations in TOPMed for the 

Weinstock* & Gopakumar* et al., Nature, 2023 manuscript. 

### Usage

After running `cargo build --release` :

`./target/release/pileup_region    `

The `` should have the following columns: `chr, pos, ref, alt, aa_change` . You 

can leave `aa_change` as blank or a dummy value if you don't need it. The column headers need to

match these exactly. 

An example file is provided here for the U2AF1 locus (`u2af1_vars.txt`) where the 

coordinates are for GRCh38. Note that the genome build of this file must match that of the 

BAM/CRAM. 

The fasta file should be the same one used to align the BAM/CRAMs. 

### Install

After cloning this repository, and installing the [Rust programming language](https://www.rust-lang.org/tools/install), run:

`cargo build --release`

It may take a few minutes to compile depending on your system. 

### Authors

Contact [Josh Weinstock](https://github.com/weinstockj)