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

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)