# 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