Introduction

bamRdf is a software which clusters reads of bam file into read families according to chromosome, start, and end position.

Preparation

htslib(https://github.com/samtools/htslib) SeqLib(https://github.com/walaj/SeqLib)

Install

git clone https://github.com/RainyEricYe/bamRdf.git
cd bamRdf
make

Citation

Rui Ye et al. LFMD: detecting low-frequency mutations in genome sequencing data without molecular tags.
https://www.biorxiv.org/content/10.1101/617381v9

Usage

Program: bamRdf (cluster read pair by positon)
Version: v1.4
Authors: yerui
Contact: yerui@connect.hku.hk

Usage: bamRdf -i in.bam

   -t [s]    target region file (bed)
   -i [s]    input original bam file which sorted by Qname
   -o [s]    output bam file [out.bam]
   -d [i]    discard reads family which size < [int]  [0]
   -b [i]    memory control: N pairs of reads as a block [3000000]
   -m        mitochondrial mode. allow read start < 0 [false]
   -n [i]    limit number of read pairs [0, unlimited]
   -v        version
   -h        help