iCopyDAV: Integrated platform for Copy number variations – Detection, Annotation and Visualization
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Readme.md

iCopyDAV: Integrated platform for Copy number variations – Detection, Annotation and Visualization

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