net.sf.varscan
Class VarScan

java.lang.Object
  net.sf.varscan.VarScan

public class VarScan
extends java.lang.Object

A set of tools for variant detection in next-generation sequence data.

Version:

2.4

Author:

Daniel C. Koboldt

 COMMANDS
 pileup2snp [pileup file] OPTIONS
                        Call SNPs from a pileup file that meet certain cutoffs
                        Input:  Pileup file and parameters
                        Output: SNPs file with read counts and p-value

 pileup2indel [pileup file] OPTIONS
                        Call indels from a pileup file that meet certain cutoffs
                        Input:  Pileup file and parameters
                        Output: Indels file with read counts and p-value

 pileup2cns [pileup file] OPTIONS
                        Call consensus genotypes (reference or variant) at sites with sufficient coverage
                        Input:  Pileup file and parameters
                        Output: Consensus file with genotypes, read counts and p-values

 mpileup2cns [pileup file] OPTIONS
                        Call consensus genotypes (reference or variant) across one or more samples
                        Input:  SAMtools mpileup file and parameters
                        Output: Consensus file with genotypes, read counts and p-values, or VCF file

 somatic [normal_pileup] [tumor_pileup] [output] OPTIONS
                        Determine somatic status of SNPs from normal/tumor pileup for positions
                        Input:  Normal pileup, tumor pileup, and positions file
                        Output: SNPs file with read counts and somatic status

 readcounts [pileup] --variants-file [positions] --output-file [output]
                        Obtain read counts for each allele of variants from a pileup file
                        Input:  Variants file and pileupfile
                        Output: Variants file with read counts for each allele

 filter [variant file] OPTIONS
                        Filter a set of SNPs/indels based on coverage, reads, p-value, etc.
                        Input:  SNPs file with read counts and p-value
                        Output: Filtered SNPs file with read counts and p-value

 somaticFilter [somatic-status file] OPTIONS
                        Filter VarScan Somatic/Germline/LOH calls for clusters and proximal indels
                        Input:  VarScan output for SNPs or Indels (varscan.output.snp)
                        Output: Variants passing all filters (varscan.output.snp.filter)

 fpFilter [variant-file] [readcount-file] OPTIONS
                        Apply the false-positive filter to VarScan variant calls
                        Input:  VarScan output for SNPs or Indels (varscan.output.snp) and bam-readcount output
                        Output: Variants passing all filters (varscan.output.snp.fpfilter)

 processSomatic [somatic-status file] OPTIONS
                        Process VarScan output by somatic status and confidence
                        Input:  VarScan output for SNPs or Indels (varscan.output.snp)
                        Output: Variants by somatic status (varscan.output.snp.Somatic)

 copyCaller [copynumber file] OPTIONS
                        Process VarScan copynumber output to adjust for GC and make preliminary calls
                        Input:  VarScan copynumber output (varscan.output.copynumber)
                        Output: Normalized copy number with preliminary calls (varscan.output.copynumber.called)

 compare [file1] [file2] [type] [output] OPTIONS
                        Compares chromosome-position entries in two tab-delimited files
                        Input:  File 1 and File 2
                        Output: Merged, intersected, or unique entries

 limit [variants] --regions-file [regions] --output-file [output]
                        Limit a tab-delimited file (SNPs, pileup, etc) to a set of positions or regions
                        Input:  tab-delimited input file with chromosome & position; positions-file or regions-file
                        Output: Entries in input-file matching regions or positions

 coverage [pileup-file] --regions-file [regions] --output-file [output]
                        **Experimental** Calculate Q>20 coverage depth/breadth for a set of target regions
                        Input:  Pileup file and tab-delimited regions-file
                        Output: Coverage report at various Q>20 depths (1x,10x,20x...)


 

Constructor Summary

VarScan()

Method Summary

static void	compare(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Compares two lists of positions/variants
static void	copyCaller(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Calls somatic copy number events from copynumber output
static void	copynumber(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Determines tumor copy number from normal and tumor pileup files
static void	coverage(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Reports region coverage from a BAM file
static void	filter(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Filters variants by coverage, significance, frequency, etc.
static void	fpfilter(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Applies false positive filter using bam-readcount information
static double	getSignificance(int obsReads1, int obsReads2) Calculates significance of read counts versus baseline error
static double	getSignificance(int expReads1, int expReads2, int obsReads1, int obsReads2) Calculates significance of read counts between two samples
static void	limit(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Limits pileup or variant files to a list of positions or regions
static void	main(java.lang.String[] args) Runs the main execution logic
static void	mpileup2call(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params, java.lang.String callType) Calls SNPs from an mpileup file
static void	pileup2call(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params, java.lang.String callType) Calls SNPs from a pileup file
static void	processSomatic(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Splits VarScan output according to somatic status and confidence
static void	readcounts(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Obtains read counts for a list of variants
static void	somatic(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Calls somatic/germline/LOH variants from normal and tumor pileup files
static void	somaticFilter(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params) Filters variants by coverage, significance, frequency, etc.
static void	trio(java.lang.String[] args, java.util.HashMap<java.lang.String,java.lang.String> params, java.lang.String callType) Calls SNPs in a father-mother-child trio from an mpileup file

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

VarScan

public VarScan()

Method Detail

main

public static void main(java.lang.String[] args)

Runs the main execution logic

Parameters:

args - Command-line arguments

pileup2call

public static void pileup2call(java.lang.String[] args,
                               java.util.HashMap<java.lang.String,java.lang.String> params,
                               java.lang.String callType)

Calls SNPs from a pileup file

Parameters:

args - Command-line arguments and parameters

callType - "SNP", "INDEL", or "CNS"

mpileup2call

public static void mpileup2call(java.lang.String[] args,
                                java.util.HashMap<java.lang.String,java.lang.String> params,
                                java.lang.String callType)

Calls SNPs from an mpileup file

Parameters:

args - Command-line arguments and parameters

callType - "SNP", "INDEL", or "CNS"

readcounts

public static void readcounts(java.lang.String[] args,
                              java.util.HashMap<java.lang.String,java.lang.String> params)

Obtains read counts for a list of variants

Parameters:

args - Command-line arguments

somatic

public static void somatic(java.lang.String[] args,
                           java.util.HashMap<java.lang.String,java.lang.String> params)

Calls somatic/germline/LOH variants from normal and tumor pileup files

Parameters:

args - Command-line arguments

trio

public static void trio(java.lang.String[] args,
                        java.util.HashMap<java.lang.String,java.lang.String> params,
                        java.lang.String callType)

Calls SNPs in a father-mother-child trio from an mpileup file

Parameters:

args - Command-line arguments and parameters

callType - "SNP", "INDEL", or "CNS"

copynumber

public static void copynumber(java.lang.String[] args,
                              java.util.HashMap<java.lang.String,java.lang.String> params)

Determines tumor copy number from normal and tumor pileup files

Parameters:

args - Command-line arguments

filter

public static void filter(java.lang.String[] args,
                          java.util.HashMap<java.lang.String,java.lang.String> params)

Filters variants by coverage, significance, frequency, etc.

Parameters:

args - Command-line arguments

fpfilter

public static void fpfilter(java.lang.String[] args,
                            java.util.HashMap<java.lang.String,java.lang.String> params)

Applies false positive filter using bam-readcount information

Parameters:

args - Command-line arguments

somaticFilter

public static void somaticFilter(java.lang.String[] args,
                                 java.util.HashMap<java.lang.String,java.lang.String> params)

Filters variants by coverage, significance, frequency, etc.

Parameters:

args - Command-line arguments

processSomatic

public static void processSomatic(java.lang.String[] args,
                                  java.util.HashMap<java.lang.String,java.lang.String> params)

Splits VarScan output according to somatic status and confidence

Parameters:

args - Command-line arguments

copyCaller

public static void copyCaller(java.lang.String[] args,
                              java.util.HashMap<java.lang.String,java.lang.String> params)

Calls somatic copy number events from copynumber output

Parameters:

args - Command-line arguments

compare

public static void compare(java.lang.String[] args,
                           java.util.HashMap<java.lang.String,java.lang.String> params)

Compares two lists of positions/variants

Parameters:

args - Command-line arguments

limit

public static void limit(java.lang.String[] args,
                         java.util.HashMap<java.lang.String,java.lang.String> params)

Limits pileup or variant files to a list of positions or regions

Parameters:

args - Command-line arguments

coverage

public static void coverage(java.lang.String[] args,
                            java.util.HashMap<java.lang.String,java.lang.String> params)

Reports region coverage from a BAM file

Parameters:

args - Command-line arguments

getSignificance

public static double getSignificance(int obsReads1,
                                     int obsReads2)

Calculates significance of read counts versus baseline error

Parameters:

obsReads1 - Reads supporting allele 1

obsReads2 - Reads supporting allele 2

Returns:

p-value P-value from Fisher's Exact Test

getSignificance

public static double getSignificance(int expReads1,
                                     int expReads2,
                                     int obsReads1,
                                     int obsReads2)

Calculates significance of read counts between two samples

Parameters:

expReads1 - Reads supporting allele 1 (expected)

expReads2 - Reads supporting allele 2 (expected)

obsReads1 - Reads supporting allele 1 (observed)

obsReads2 - Reads supporting allele 2 (observed)

Returns:

p-value P-value from Fisher's Exact Test