mpileup
| Crates.io | mpileup |
| lib.rs | mpileup |
| version | 0.0.28 |
| created_at | 2021-06-23 06:16:35.276236+00 |
| updated_at | 2022-09-12 06:46:21.904446+00 |
| description | Pile up multiple bam files site by site |
| homepage | |
| repository | |
| max_upload_size | |
| id | 413806 |
| size | 1,344,748 |
Chang Y (y9c)
documentation
https://docs.rs/crate/mpileup/latest
README
mpileup
Install
cargo install mpileup
Usage
pileup number of base and indel
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.faas 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
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
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)