Given a BAM or PAM, and a BED file describing genomic positions of interest, bio-pileup reports the number of reads supporting each allele at each position. This command is similar to "bcftools mpileup".

There are options for "collapsing" the two ends of a read-pair together, or entire duplicate-sets ("bags") identified by doppelmark.

Only SNPs are currently reported, but indel support is very likely to be added in the future.

Sample usage: bio-pileup
--bed my-regions.bed
--out output-prefix
my.bam
ref.fa

Run "bio-pileup --help" for more details.