Yf tumor only (#1298)
* tumor only pipeline * a few new wrappers for picard tools
This commit is contained in:
Yossi Farjoun
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3ecaacd8ec
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/*
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* Copyright 2012-2016 Broad Institute, Inc.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.gatk.queue.extensions.picard
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import java.io.File
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import htsjdk.samtools.ValidationStringency
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import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
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import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
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/**
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* Reads a VCF/VCF.gz/BCF and and filters it quickly based on some simple hard filters
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*/
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class FilterVcf extends JavaCommandLineFunction {
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analysisName = "FilterVcf"
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javaMainClass = "picard.vcf.FilterVcf"
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@Input(doc = "The input VCF files to filter.", shortName = "input", fullName = "input_vcf_file", required = true)
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var input: File = _
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@Output(doc = "The output VCF which will have it's FILTER field updated", required = false)
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var output: File = _
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@Argument(doc = "The minimum allele balance acceptable before filtering a site. Allele balance is calculated for heterozygotes as " +
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"the number of bases supporting the least-represented allele over the total number of base observations. Different heterozygous " +
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"genotypes at the same locus are measured independently. The locus is filtered if any allele balance is below the limit.", required = false)
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var minAb: Option[Double] = _
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@Argument(doc = "The minimum sequencing depth supporting a genotype before the genotype will be filtered out.", required = false)
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var minDp: Option[Double] = _
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@Argument(doc = "The minimum genotype quality that must be achieved for a sample otherwise the genotype will be filtered out.", required = false)
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var minGQ: Option[Double] = _
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@Argument(doc = "The maximum phred scaled fisher strand value before a site will be filtered out.", required = false)
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var maxFs: Option[Double] = _
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@Argument(doc = "The minimum QD value to accept or otherwise filter out the variant.", required = false)
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var minQd: Option[Double] = _
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var validationStringency = ValidationStringency.SILENT
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var compressionLevel: Option[Int] = None
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var createIndex: Option[Boolean] = None
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var maxRecordsInRam: Option[Int] = None
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var assumeSorted: Option[Boolean] = None
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override def commandLine = super.commandLine +
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required("INPUT=", input, spaceSeparated = false) +
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required("TMP_DIR=" + jobTempDir) +
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optional("OUTPUT=", output, spaceSeparated = false) +
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optional("MIN_AB=", minAb, spaceSeparated = false) +
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optional("MIN_DP=", minDp, spaceSeparated = false) +
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optional("MIN_GQ=", minGQ, spaceSeparated = false) +
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optional("MIN_FS=", maxFs, spaceSeparated = false) +
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optional("MIN_QD=", minQd, spaceSeparated = false) +
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optional("COMPRESSION_LEVEL=", compressionLevel, spaceSeparated = false) +
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optional("VALIDATION_STRINGENCY=", validationStringency, spaceSeparated = false) +
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optional("MAX_RECORDS_IN_RAM=", maxRecordsInRam, spaceSeparated = false) +
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optional("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
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optional("CREATE_INDEX=", createIndex, spaceSeparated = false)
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}
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@ -0,0 +1,68 @@
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/*
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* Copyright 2012-2016 Broad Institute, Inc.
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.gatk.queue.extensions.picard
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import java.io.File
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import htsjdk.samtools.ValidationStringency
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import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
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import org.broadinstitute.gatk.utils.commandline.{Argument, Input, Output}
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/**
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* "Reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information,
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* including annotations based on genotypes (e.g. AN, AF). Output can be any support variant format including .vcf, .vcf.gz or .bcf."
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*/
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class MakeSitesOnlyVcf extends JavaCommandLineFunction {
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analysisName = "MakeSitesOnlyVcf"
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javaMainClass = "picard.vcf.MakeSitesOnlyVcf"
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@Input(doc = "The input VCF files to analyze.", shortName = "input", fullName = "input_vcf_file", required = true)
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var input: File = _
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@Output(doc = "The output VCF which will not have any genotypes, but will keep the INFO field intact.", required = false)
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var output: File = _
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@Argument(shortName = "S", doc = "Optionally one or more samples to retain when building the \'sites-only\' VCF.", required = false)
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var samples: List[String] = _
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var validationStringency = ValidationStringency.SILENT
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var compressionLevel: Option[Int] = None
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var createIndex: Option[Boolean] = None
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var maxRecordsInRam: Option[Int] = None
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var assumeSorted: Option[Boolean] = None
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override def commandLine = super.commandLine +
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required("INPUT=", input, spaceSeparated = false) +
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required("TMP_DIR=" + jobTempDir) +
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optional("OUTPUT=", output, spaceSeparated = false) +
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repeat("SAMPLE=", samples, spaceSeparated = false) +
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optional("COMPRESSION_LEVEL=", compressionLevel, spaceSeparated = false) +
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optional("VALIDATION_STRINGENCY=", validationStringency, spaceSeparated = false) +
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optional("MAX_RECORDS_IN_RAM=", maxRecordsInRam, spaceSeparated = false) +
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optional("ASSUME_SORTED=", assumeSorted, spaceSeparated = false) +
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optional("CREATE_INDEX=", createIndex, spaceSeparated = false)
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}
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