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Vecuum

Vecuum is a Java based variant caller designed for detecting contamination-induced point mutations from hybrid-capture-based genome sequencing data (e.g. WGS, WES, targeted capture, etc). Vecuum is specialized for identifying false variants caused by recombinant vector contamination, however, can be applied to detect spurious calls for various external contaminants such as xenogeneic genomes, cDNA libraries, or even pseudogenes.
The important features of Vecuum are:

Estimation of the genomic location of vector-contaminated regions
Identification of false variants originated from vector inserts

Get the most recent version of Vecuum here:

Update note (Last updated 02-08-2016)

Vecuum-1.0.1 (02-08-2016) *Minor Update

Improvements:

GRCh38 is now supported with '-a' option.
The version of prerequisite softwares is updated. Previous version of SAMtools (0.1.x) can also be used if the path contains version information (e.g. -S /utils/samtools-0.1.19/samtools)
A few minor bugs including output file naming, presenting transcript ID rather than gene ID, typos in result files have been fixed.
Added "Reccomendation" sections for the first-time users. We highly recommend to use '-A -k' options to analyze entire genome, rather default setttings. A few false variants can be observed regardless of contamination due to the processed pseudogenes.

Prerequisite softwares

Installation of Vecuum

Vecuum was developed using JAVA JDK 7 64bit. To run Vecuum, Java Runtime Environment (JRE) version 1.7.x or later is required. Download the most recent version of Vecuum program in the code page and extract the gzipped archive.

tar -zxvf Vecuum-1.x.y.tar.gz

It contains the followings:

Vecuum.jar
: Executable JAR file of Vecuum
README.txt
: Nothing much in this file currently. Please refer to this page instead.
lib/
: directory containing other JAR libraries for Vecuum
database/
: directory containing database files for Vecuum

Running Vecuum

To run Vecuum, you can simply run the JAR executable file like below:

java -jar Vecuum.jar

The -h or -? options will bring the following usage of Vecuum. If you see this, you are ready to run Vecuum.

Vecuum: Contamination-induced false variant caller
Version: 1.0.1
Usage: java -jar Vecuum.jar -r <reference_genome.fa> -b <sample_sorted_indexed.bam> -B <bwa_path> -S <samtools_path> [options]

Input options:

-r PATH     path for indexed reference genome FASTA [.fa/.fasta]
-b PATH     path for indexed bam file [.bam]
-B PATH     path for bwa (e.g. /usr/bin/bwa)
-S PATH     path for samtools (e.g. /usr/bin/samtools)
-t PATH     path for indexed transcriptome FASTA [.fa/.fasta]
-g PATH     path for reference genome GTF file [.gtf]
-u PATH     path for unmapped bam file [.bam]
-R PATH     path for region of interest list [tab-delimited text (chr   start   end gene_name)]
-V PATH     path for suspicious variant list [tab-delimited text (chr   pos)]
-a STR      Assembly version of reference genome [hg19]

Analysis parameters for vector contamination assessment:

-n INT      Number of threads for bwa-mem [1]
-p INT      padding size [5]
-Q INT      mapQ threshold [30]
-l INT      minMatchLen [20]
-s INT      minVectorInsertSupportCnt [3]
-i INT      minVectorInsertSize [500]
-I INT      maxVectorInsertSize [500000]
-k          Skip vector checking step [must be used with -R or -A option]

Analysis parameters for false variant detection:

-A          Searching false variants for all exons regardless of vector contamination
-q INT      baseQ threshold [20]
-c INT      minVectorBalleleCnt [3]
-C INT      maxSampleBalleleCnt [3]
-f FLOAT    minVectorBAF [0.01]
-F FLOAT    maxSampleBAF [0.01]
-d INT      minSampleDepth [5]

Output options:

-o PATH     path for output directory [bam file directory]
-O          Report vector filtered bam file

Recommendation

If you have a list of genes that can be plausible regions of contamination, we recommend to use -R and -k options to reduce the computation times.

java -jar Vecuum.jar -r <reference_genome.fa> -b <sample_sorted_indexed.bam> -B <bwa_path> -S <samtools_path> -R <tab-delimeted gene list (chr start end gene_name)> -k

If you want to detect all false variants for entire genome, we highly recommend to use -A and -k options rather than default running.

java -jar Vecuum.jar -r <reference_genome.fa> -b <sample_sorted_indexed.bam> -B <bwa_path> -S <samtools_path> -A -k

Inputs and options

Mandatory inputs:

There are three mandatory inputs for Vecuum.

Input	Option	Description
Reference sequence	-r	FASTA formatted reference sequence file. The reference must be BWA indexed.
Sample sequence data	-b	BAM formatted alignment file for sample. The BAM file must be (coordinate) sorted and indexed.
BWA executable file	-B	BWA executable file path (absolute path).
SAMtools executable file	-S	SAMtools executable file path (absolute path).

Options:

There are several options you can give to Vecuum for more accurate running.

Option	Default Value	Description
-t	none (provided in the database folder)	FASTA formatted transcriptome file for the detection of ve-reads. The FASTA file must be indexed.
-g	none (provided in the database folder)	GTF file for exon information
-u		Path for the unmapped BAM file (if unmapped reads are separated. e.g. 1KG data)
-R		Tab-delimited text file for region of interest [tab-delimited text (chr start end gene_name)]. False variant detection must be processed for these regions regardless of the result of vector contamination assessment.
-V		Tab-delimited text file for suspicious variant [tab-delimited text (chr pos)]. Statistics will be reported for these variants regardless of the result of false variant detection.
-a	hg19	Assembly version of used reference genome (hg19/GRCh37, hg38/GRCh38)