Skip to content
/ mpileup Public

extract nucleotide/read counts at user specific loci from multiple bam files

License

Notifications You must be signed in to change notification settings

y9c/mpileup

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

69 Commits
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

Crates.io Crates.io docs.rs

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.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

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

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)

About

extract nucleotide/read counts at user specific loci from multiple bam files

Topics

Resources

License

Stars

Watchers

Forks

Sponsor this project

Packages

No packages published