https://github.com/y9c/mpileup
extract nucleotide/read counts at user specific loci from multiple bam files
https://github.com/y9c/mpileup
bam modification mutation rust snp
Last synced: 3 months ago
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extract nucleotide/read counts at user specific loci from multiple bam files
- Host: GitHub
- URL: https://github.com/y9c/mpileup
- Owner: y9c
- License: gpl-3.0
- Created: 2021-06-23T06:17:34.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2022-09-12T20:00:02.000Z (over 2 years ago)
- Last Synced: 2025-01-13T01:48:55.504Z (5 months ago)
- Topics: bam, modification, mutation, rust, snp
- Language: Rust
- Homepage:
- Size: 521 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Funding: .github/FUNDING.yml
- License: LICENSE.md
Awesome Lists containing this project
README
[](https://crates.io/crates/mpileup)
[](https://crates.io/crates/mpileup)
[](https://docs.rs/mpileup)
# mpileup
## Install
```bash
cargo install mpileup
```
## Usage
### pileup number of base and indel
```bash
mpileup base --target test/region.bed --reference test/reference.fa --input test/sample1.bam test/sample2.bam -g -d 10
```
In this subcommand (example),
- pileup up reads within region in `region.bed`
- use `reference.fa` as reference
- accept **multiple** input bam files: `sample1.bam`, `sample2.bam` ...
- report indel with argument `-g`
- set depth cutoff as 10 by `-d 10`
### count number of reads
```bash
mpileup count --target test/region.bed --reference test/reference.fa --input test/sample1.bam
```
In this subcommand (example),
- only support one file a time
## Documentation
[Read more](https://docs.rs/crate/mpileup/latest)
## TODO
- support sam flag filtering
- support trimming read ends
- remove duplicate by UMI on qname
- group the result by customized tag (such as cell barcode)