cargo install mpileup
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
mpileup count --target test/region.bed --reference test/reference.fa --input test/sample1.bam
In this subcommand (example),
- only support one file a time
- support sam flag filtering
- support trimming read ends
- remove duplicate by UMI on qname
- group the result by customized tag (such as cell barcode)