Introduction

bamDCS is a software which generates double strand consensus reads for low-frequency mutation. The input files are from bamRdf.

Preparation

• htslib(https://github.com/samtools/htslib)

• SeqLib(https://github.com/walaj/SeqLib)

• alglib(http://www.alglib.net/translator/re/alglib-3.15.0.cpp.gpl.tgz)

Install

git clone https://github.com/RainyEricYe/bamDCS.git
cd bamDCS
vi Makefile && change filepath of libs
make

if errors occur, try
conda activate lfmd
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: bamDCS  (generate double strand consensus reads for low-frequency mutation)
Version: v2.4
Authors: yerui
Contact: yerui@connect.hku.hk

Options: bamDCS in.bam outprefix

    -q [i]     base quality cutoff [20]
    -Q [i]     map quality cutoff [30]
    -s [i]     min support num on each strand [3]
    -S [i]     max support num on each strand [3000]
    -N [f]     max fraction of N on consensus read [0.1]
    -f [f]     min fraction of alterative allele in a read family [0.002]
    -e [f]     precision of allele frequency while calculate likelihood ratio [0.00001]
    -g [f]     gap between likelihood ratios of major and rest genotypes [2.0]
    -x [i]     Encoding offset for phred quality scores [33]
    -t [i]     min support num to construct a haplotype seq [3]
    -c         discard soft-clipping reads [false]
    -C [i]     soft trim N base from both ends of read [5]
    -p [f]     expected PCR error rate during library construction [1e-5]
    -n [i]     N read pairs to be randomly selected and used [0, total]
    -o [s]     output bam File directly []
    -a         output single pair-end reads [false]
    -b         output SSCS [false]
    -d         debug mode [false]
    -h         help
    -v         version