varscan_wrapper: varscan/varscan

annotate varscan/varscan_somatic.xml @ 4:572397bbe057 draft default tip

Added Xmx10G setting to both varscan_somatic wrappers

author	geert-vandeweyer
date	Wed, 26 Mar 2014 05:24:22 -0400
parents
children

rev	line source
4 572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	1 <tool id="varscan_somatic_vcf" name="VarScan Somatic (VCF Output)" version="2.3.5">
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	2 <description>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	3 somatic mutation caller for cancer genomics
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	4 </description>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	5 <requirements>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	6 <requirement type="package" version="2.3.5">VarScan</requirement>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	7 </requirements>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	8 <command interpreter="perl">
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	9
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	10 varscan_somatic.pl
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	11 "COMMAND::java -Xmx10G -jar \$JAVA_JAR_PATH/VarScan.v2.3.5.jar somatic"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	12 "NORMAL::$normal"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	13 "TUMOR::$tumor"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	14 "TUMORBAM::$tumorbam"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	15 "OUTPUT::$output"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	16 "LOG::$log"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	17
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	18 "OPTION::--min-coverage $min_coverage"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	19 "OPTION::--min-coverage-normal $min_coverage_normal"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	20 "OPTION::--min-coverage-tumor $min_coverage_tumor"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	21
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	22 "OPTION::--min-var-freq $min_var_freq"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	23 "OPTION::--min-freq-for-hom $min_freq_for_hom"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	24
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	25 "OPTION::--normal-purity $normal_purity"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	26 "OPTION::--tumor-purity $tumor_purity"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	27
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	28 "OPTION::--p-value $p_value"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	29 "OPTION::--somatic-p-value $somatic_p_value"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	30
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	31 "OPTION::--strand-filter $strand_filter"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	32 "OPTION::--validation $validation"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	33 "OPTION::--output-vcf 1"
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	34
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	35
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	36
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	37 </command>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	38
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	39 <inputs>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	40
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	41 <param name="normal" type="data" format="pileup" label="normal mpileup file" help="The SAMtools mpileup file for normal sample" />
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	42 <param name="tumor" type="data" format="pileup" label="tumor mpileup file" help="The SAMtools mpileup file for tumor sample" />
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	43 <param name="tumorbam" type="data" format="bam" label="tumor BAM file" help="The BAM file of the tumor sample used in mpileup step" />
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	44
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	45 <param name="min_coverage" type="integer" label="min-coverage" help="" optional="true" value="8"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	46 <param name="min_coverage_normal" type="integer" label="min-coverage-normal" help="" optional="true" value="8"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	47 <param name="min_coverage_tumor" type="integer" label="min-coverage-tumor" help="" optional="true" value="6"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	48
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	49 <param name="min_var_freq" type="float" label="min-var-freq" help="" optional="true" value="0.10"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	50 <param name="min_freq_for_hom" type="float" label="min-freq-for-hom" help="" optional="true" value="0.75"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	51
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	52 <param name="normal_purity" type="float" label="normal-purity" help="" optional="true" value="1.00"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	53 <param name="tumor_purity" type="float" label="tumor-purity" help="" optional="true" value="1.00"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	54
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	55
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	56 <param name="p_value" type="text" label="p-value" help="" optional="true" value="0.99"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	57 <param name="somatic_p_value" type="text" label="somatic-p-value" help="" optional="true" value="0.05"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	58
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	59 <param name="strand_filter" type="integer" label="strand-filter" help="" optional="true" value="1"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	60 <param name="validation" type="integer" label="validation" help="" optional="true" value="0"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	61
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	62 </inputs>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	63 <outputs>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	64 <data type="data" format="vcf" name="output" label="${tool.name} result on ${on_string}"/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	65 <data type="data" format="txt" name="log" label="${tool.name} result on ${on_string} (log) "/>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	66 <!--<data type="data" format="txt" name="snp" label="${tool.name} result on ${on_string} (SNP file)" />
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	67 <data type="data" format="txt" name="indel" label="${tool.name} result on ${on_string} (INDEL file)" />-->
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	68
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	69
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	70 </outputs>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	71
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	72 <help>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	73
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	74 .. class:: infomark
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	75
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	76 What it does
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	77
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	78 ::
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	79
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	80 VarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments. The newest version, VarScan 2, is written in Java, so it runs on most operating systems. It can be used to detect different types of variation:
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	81
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	82 Germline variants (SNPs an dindels) in individual samples or pools of samples.
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	83 Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	84 Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	85 Somatic copy number alterations (CNAs) in tumor-normal exome data.
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	86
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	87
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	88 Input
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	89
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	90 ::
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	91
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	92 mpileup normal file - The SAMtools mpileup file for normal
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	93 mpileup tumor file - The SAMtools mpileup file for tumor
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	94
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	95
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	96 Parameters
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	97
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	98 ::
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	99
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	100 min-coverage
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	101 Minimum read depth at a position to make a call [8]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	102
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	103 min-coverage-normal
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	104 Minimum coverage in normal to call somatic [8]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	105
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	106 min-coverage-tumor
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	107 Minimum coverage in tumor to call somatic [6]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	108
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	109 min-var-freq
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	110 Minimum variant frequency to call a heterozygote [0.10]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	111
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	112 min-freq-for-hom
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	113 Minimum frequency to call homozygote [0.75]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	114
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	115 normal-purity
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	116 Estimated purity (non-tumor content) of normal sample [1.00]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	117
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	118 tumor-purity
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	119 Estimated purity (tumor content) of tumor sample [1.00]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	120
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	121 p-value
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	122 Default p-value threshold for calling variants [0.99]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	123
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	124 somatic-p-value
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	125 P-value threshold to call a somatic site [0.05]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	126
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	127 strand-filter
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	128 If set to 1, removes variants with >90% strand bias
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	129
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	130 validation
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	131 If set to 1, outputs all compared positions even if non-variant
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	132
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	133 output-vcf
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	134 If set to 1, outputs in VCF format [Default]
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	135
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	136
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	137
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	138 </help>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	139 </tool>
572397bbe057 Added Xmx10G setting to both varscan_somatic wrappers geert-vandeweyer parents: diff changeset	140

Mercurial > repos > geert-vandeweyer > varscan_wrapper

annotate varscan/varscan_somatic.xml @ 4:572397bbe057 draft default tip