Introduces simulated allele-specific copy number variants into exome and targeted sequence data sets

Soroush Samadian

Suluxan Mohanraj suluxan.mohanraj@uhnresearch.ca

Bamgineer is a tool that can be used to introduce user-defined haplotype-phased allele-specific copy number variations (CNV) into an existing Binary Alignment Mapping (BAM) file and demonstrated applicability to simulate somatic cancer CNVs in exome and targeted cell- free DNA sequencing data sets. This is done by introducing new read pairs sampled from existing reads, thereby retaining biases of the original data such as local coverage, strand bias, and insert size. As input, Bamgineer requires a BAM file and two lists of non- overlapping genomic coordinates to introduce allele-specific gains and losses. The user may explicitly provide known haplotypes or chose to use the BEAGLE phasing module that is already incorporated within Bamgineer. We implemented parallelization of the Bamgineer algorithm for both standalone and high performance computing cluster environments, significantly improving the scalability of the algorithm.Bamgineer has been extensively tested on whole exome sequencing and targeted gene panel applied to cell-free DNA sequencing data.

Quick start: Quick start

If you have any questions with the package, please feel free to post in our Google user group https://groups.google.com/d/forum/bamgineer or email us at bamgineer@googlegroups.com. We will try our best to reply as soon as possible.

Below is a general description of the file formats and prerequizites. For details on usage and example, please follow our detailed guide in Quick start

    usage: python simulate.py [-h] [--inbam INPUT_BAM] [--outbam OUTPUT_BAM]
                     [--cnvgain CNV_GAIN_FILE] [--cnvloss CNV_LOSS_FILE] [--splitdir BAM_SPLIT_DIR] 
                     [--config CONFIG_FILE] [--cancer CANCER_TYPE][--phase PHASE] [--ctdna CT_DNA]
                     
    
    arguments:
       -inbam  INPUT_BAM ,         bam file from for input
       -outbam OUTPUT_BAM,         bam file name for output
       -config CONFIG_FILE,        configuration file including paths to executables and references
       -cnv_bed CNV_BED_FILE,       bed file name containing non-overlapping gain and loss regions
       
    optional arguments:
       -h, -help                  show this help message and exit
       -cancertype CANCER_TYPE,    cancer type/acronym
       -splitdir BAM_SPLIT_DIR,    input bam split by chromosomes
       -p PHASE,                   whether SNP phasing should be applied
       -ctdna CT_DNA,              whether simulation is on reads obtained from ctDNA sequencing data   

General NGS tools

Samtools (version 1.2): samtools
Bedtools:bedtools
VCFtools:vcftools
BamUtil:bamutil

Python packages

pysam (version 0.8.4): pysam
Note: the latest version of pysam (0.9.0) is not backward compatible with Samtools1.2
pyVCF pyvcf
pyBedTools pybedtools

Input parameters

-inbam: input sorted and indexed normal bam file
-cnv_amp: bed file for allele-specific and cancer-specific CNV amplifications (null is not specified)
-cnv_del: bed file for allele-specific and cancer-specific CNV deletions (null is not specified)
-vcf: normal heterozygous vcf file (could be from HaplotypeCaller output, not including indels and homozygous loci)
-target_region: bed file containing the target regions (exons or any user-specified region) \ -phased(optional): Binary flag to perform phasing (BEAGLE) of SNPs prior to spiking CNV's

Output

-outbam: output engineered, sorted bam file