iCopyDAV: Integrated platform for Copy number variations

March 6, 2018 · View on GitHub

Version -1 for CNV detection Pipeline

RD based CNV detection tool

Requirements

Make sure that these tools are added to your PATH variable

samtools (link)
bedtools (>=2.26) (link)
openMPI (Installation Guide)
R-packages - DNAcopy, ParDNAcopy, quantsmooth, GenomicAlignments, rtracklayer

Installation

Download the source code from https://github.com/vogetihrsh/icopydav, extract the zip file

unzip iCopyDAV.zip
cd iCopyDAV
make

Please download annotations from http://bioinf.iiit.ac.in/icopydav/ and add the folder to working directory.

Usage

# CALCULATE OPTIMAL BIN/WINDOW SIZE
./calOptBinSize -c <config file> -i <input BAM>

# DATA PREPARATION
./prepareData -m <mappability file> -g <gc content file> --win <desired window size> --genome_file <Genome file> -o <Output file name prefix>

# PRETREATMENT STEP
./pretreatment -i <input BAM> -z <bed file containing bins> --mapfile < file contaning mappability values> -o <output prefix> --gcfile <file containing GC scores>

# SEGMENTATION
./runSegmentation -o <output prefix> <-t or -d or both>

# POSTPROCESSING AND CNV CALLING
./callCNV -o <output prefix> -z <bed file contaning bins> <genome flag (--hg18 or --hg19)>

# ANNOTATION 
./annotate -i <input bed file> -o <output prefix> <genome flag (--hg18 or --hg19)>

# PLOT
./plot -i <input bed file> -o <output file name> <genome flag (--hg18 or --hg19)>
./plot -i <input bed file> -d --start <start position> --end <end position> -o <output file name> <genome flag (--hg18 or --hg19)>

Note:

Pretreatment, runSegmentation, callCNV should have same value for the parameter -o.

calOptBinSize

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-c	Yes/STRING	Config file contaning parameters to be used for calculations. Parameters similarity to those used in ReadDepth config file. For additional info, please refer to "config.txt" in the source directory.	Required
-i	Yes/STRING	Input BAM File.	Required
- -help	No/-	Prints usage statement. Should be exclusively used.	Optional

prepareData

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-m	Yes/STRING	Mappability score file available for 100 bp	Required
-g	Yes/STRING	GC content score file availabled for 100 bp	Required
--win	Yes/INTEGER	Desired window size for CNV predictions	Required
--genome_file	Yes/STRING	A tab-separated genome file containing chromosome number and size of the chromosome	Required
-o	Yes/STRING	Output file name that is used as prefix for coordinate, GC content and mappability files generated	Required

pretreatment

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-i	Yes/STRING	Input BAM File.	Required
-o	Yes/STRING	Output Prefix.	Required
-z	Yes/STRING	Bed file contanning bins.	Required
--mapfile	Yes/STRING	File contaning mappability values ([0,1]) of bins present in the file passed as value to -z.	Required
-p	Yes/INTEGER	Default Value: 32. Number of processes to be created for parallelization.	Optional
- -help	No/-	Prints usage statement. Should be exclusively used.	Optional
-y	No/-	When used Yoon et al. method for GC correction and mappability correction is applied to the data	Optional
--medianGC	No/-	Use Median-based method (Yoon et al) for GC correction	Optional
--medianMap	No/-	Use Median-based method (Yoon et al) for Mappability correction	Optional
--loessGC	No/-	Use Loess method to correct GC-Bias	Optional
--gcfile	No/-	File containing GC content values ([0,1]) generated in prepareData, required when using LoessGC/medianGC options	Optional

runSegmentation

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-o	Yes/STRING	Output Prefix.	Required
-p	Yes/INTEGER	Default Value: 32. Number of processes to be created for parallelization.	Optional
-t	No/-	When this flag is specified Total Variation Minimization algorithm is used for segmentation.	Atleast one of -t and -d should be used.
-d	No/-	When this flag is specified Circular Binary Segmentation algorithm is used for segmentation.	Atleast one of -t and -d should be used.
- -help	No/-	Prints usage statement. Should be exclusively used.	Optional

callCNV

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-o	Yes/STRING	Output Prefix.	Required
-z	Yes/STRING	Bed file contanning bins.	Required
--hg18	No/-	For hg18 genome. This flag will be used for getting the gap info (hg18_gap.bed) from the annotations directory.	Not required when --hg19 or --genome is used.
--hg19	No/-	For hg19 genome. This flag will be used for getting the gap info (hg19_gap.bed) from the annotations directory.	Not required when --hg18 or --genome is used.
--genome	No/-	For genomes other than hg18 and hg19. This flag will be used for getting the gap info (_gap.bed) from the annotations directory.	Not required when --hg19 or --hg18 is used.
- -help	No/-	Prints usage statement. Should be exclusively used.	Optional

annotate

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-i	Yes/STRING	Input bed file contaning regions that needed to be annotated.	Required
-o	Yes/STRING	Output prefix for the generated bed file.	Required
--hg18	No/-	hg18 genome flag. When used checks for the files contaning gene info (hg18.bed), DGV annotations (hg18DGV.bed), location annotation (hg18LocInfo.bed and gap annotations (hg18_gap.bed) in the annotation directory	Not required when --hg19 or --genome is used.
--hg19	No/-	hg19 genome flag. When used checks for the files contaning gene info (hg19.bed), DGV annotations (hg19DGV.bed), location annotation (hg19LocInfo.bed and gap annotations (hg19_gap.bed) in the annotation directory	Not required when --hg18 or --genome is used
--genome	Yes/STRING	Any genome other than hg18 and hg19 can be specified through this flag. It requires .bed, DGV.bed, _gap.bed and LocInfo.bed files to be present in annotation directory.	Not required when --hg18 or --hg19 is used.
--annDir	Yes/STRING	Default: "SOURCEDIR/annotations". Path to the annotation directory.	Optional
--help	No/-	Prints usage statement. Should be exclusively used.	Optional

plot

FLAG	REQUIRES VALUE/TYPE	DESCRIPTION	OPTIONAL/REQUIRED
-i	Yes/STRING	Input bed file containing CNV cooridnates for visualization	Required
-o	Yes/STRING	Output file name prefix for the image file generated	Required
--hg18	No/-	For hg18 genome.	Not requires when --hg19 is used
--hg19	No/-	For hg19 genome.	Not required when --hg18 is used
-d	Yes/-	User may use this parameter for visualiing CNVs within specific user-defined coordinates	Optional, required when start and end coordinates are used
--start	Yes/INTEGER	Start coodinate	Optional
--end	Yes/INTEGER	Stop coordinate	Optional

Contact

For any queries drop a mail @ vogetisri.harsha@research.iiit.ac.in