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

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)