mpileup

Install

bash cargo install mpileup

Usage

count number of base and indel

bash mpileup --target test/region.bed --reference test/reference.fa --input test/sample1.bam test/sample2.bam -g -d 10

In this examples,

• 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