VcfFilter.scala 9.33 KB
Newer Older
Peter van 't Hof's avatar
Peter van 't Hof committed
1
package nl.lumc.sasc.biopet.tools
Peter van 't Hof's avatar
Peter van 't Hof committed
2
3
4

import htsjdk.variant.variantcontext.writer.AsyncVariantContextWriter
import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder
5
6
import htsjdk.variant.vcf.{ VCFHeader, VCFFileReader }
import htsjdk.variant.variantcontext.VariantContext
Peter van 't Hof's avatar
Peter van 't Hof committed
7
import java.io.File
Peter van 't Hof's avatar
Peter van 't Hof committed
8
import java.util.ArrayList
Peter van 't Hof's avatar
Peter van 't Hof committed
9
import nl.lumc.sasc.biopet.core.BiopetJavaCommandLineFunction
Peter van 't Hof's avatar
Peter van 't Hof committed
10
import nl.lumc.sasc.biopet.core.ToolCommand
Peter van 't Hof's avatar
Peter van 't Hof committed
11
12
13
14
15
16
17
18
19
import nl.lumc.sasc.biopet.core.config.Configurable
import org.broadinstitute.gatk.utils.commandline.{ Output, Input }
import scala.collection.JavaConversions._

class VcfFilter(val root: Configurable) extends BiopetJavaCommandLineFunction {
  javaMainClass = getClass.getName

  @Input(doc = "Input vcf", shortName = "I", required = true)
  var inputVcf: File = _
Peter van 't Hof's avatar
Peter van 't Hof committed
20

Peter van 't Hof's avatar
Peter van 't Hof committed
21
22
  @Output(doc = "Output vcf", shortName = "o", required = false)
  var outputVcf: File = _
Peter van 't Hof's avatar
Peter van 't Hof committed
23

Peter van 't Hof's avatar
Peter van 't Hof committed
24
25
26
27
  var minSampleDepth: Option[Int] = _
  var minTotalDepth: Option[Int] = _
  var minAlternateDepth: Option[Int] = _
  var minSamplesPass: Option[Int] = _
Peter van 't Hof's avatar
Peter van 't Hof committed
28
  var filterRefCalls: Boolean = _
Peter van 't Hof's avatar
Peter van 't Hof committed
29

Peter van 't Hof's avatar
Peter van 't Hof committed
30
31
  override val defaultVmem = "8G"
  memoryLimit = Option(4.0)
Peter van 't Hof's avatar
Peter van 't Hof committed
32

Peter van 't Hof's avatar
Peter van 't Hof committed
33
34
35
36
37
  override def afterGraph {
    minSampleDepth = config("min_sample_depth")
    minTotalDepth = config("min_total_depth")
    minAlternateDepth = config("min_alternate_depth")
    minSamplesPass = config("min_samples_pass")
Peter van 't Hof's avatar
Peter van 't Hof committed
38
    filterRefCalls = config("filter_ref_calls")
Peter van 't Hof's avatar
Peter van 't Hof committed
39
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
40
41
42

  override def commandLine = super.commandLine +
    required("-I", inputVcf) +
Peter van 't Hof's avatar
Peter van 't Hof committed
43
    required("-o", outputVcf) +
Peter van 't Hof's avatar
Peter van 't Hof committed
44
45
    optional("--minSampleDepth", minSampleDepth) +
    optional("--minTotalDepth", minTotalDepth) +
Peter van 't Hof's avatar
Peter van 't Hof committed
46
    optional("--minAlternateDepth", minAlternateDepth) +
Peter van 't Hof's avatar
Peter van 't Hof committed
47
48
    optional("--minSamplesPass", minSamplesPass) +
    conditional(filterRefCalls, "--filterRefCalls")
Peter van 't Hof's avatar
Peter van 't Hof committed
49
50
}

Peter van 't Hof's avatar
Peter van 't Hof committed
51
object VcfFilter extends ToolCommand {
52
53
54
55
56
57
58
59
60
  case class Args(inputVcf: File = null,
                  outputVcf: File = null,
                  minSampleDepth: Int = -1,
                  minTotalDepth: Int = -1,
                  minAlternateDepth: Int = -1,
                  minSamplesPass: Int = 0,
                  minBamAlternateDepth: Int = 0,
                  mustHaveVariant: List[String] = Nil,
                  denovoInSample: String = null,
Peter van 't Hof's avatar
Peter van 't Hof committed
61
                  diffGenotype: List[(String, String)] = Nil,
62
                  filterHetVarToHomVar: List[(String, String)] = Nil,
63
64
                  filterRefCalls: Boolean = false,
                  filterNoCalls: Boolean = false) extends AbstractArgs
Peter van 't Hof's avatar
Peter van 't Hof committed
65
66

  class OptParser extends AbstractOptParser {
Peter van 't Hof's avatar
Peter van 't Hof committed
67
68
    opt[File]('I', "inputVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
      c.copy(inputVcf = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
69
    } text ("Input vcf file")
Peter van 't Hof's avatar
Peter van 't Hof committed
70
71
    opt[File]('o', "outputVcf") required () maxOccurs (1) valueName ("<file>") action { (x, c) =>
      c.copy(outputVcf = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
72
73
    } text ("Output vcf file")
    opt[Int]("minSampleDepth") unbounded () valueName ("<int>") action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
74
      c.copy(minSampleDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
75
76
    } text ("Min value for DP in genotype fields")
    opt[Int]("minTotalDepth") unbounded () valueName ("<int>") action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
77
      c.copy(minTotalDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
78
79
    } text ("Min value of DP field in INFO fields")
    opt[Int]("minAlternateDepth") unbounded () valueName ("<int>") action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
80
      c.copy(minAlternateDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
81
82
    } text ("Min value of AD field in genotype fields")
    opt[Int]("minSamplesPass") unbounded () valueName ("<int>") action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
83
      c.copy(minSamplesPass = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
84
85
    } text ("Min number opf samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth")
    opt[Int]("minBamAlternateDepth") unbounded () valueName ("<int>") action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
86
      c.copy(minBamAlternateDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
87
88
    } // TODO: Convert this to more generic filter
    opt[String]("denovoInSample") maxOccurs (1) unbounded () valueName ("<sample>") action { (x, c) =>
89
      c.copy(denovoInSample = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
90
91
    } text ("Only show variants that contain unique alleles in compete set for given sample")
    opt[String]("mustHaveVariant") unbounded () valueName ("<sample>") action { (x, c) =>
92
      c.copy(mustHaveVariant = x :: c.mustHaveVariant)
Peter van 't Hof's avatar
Peter van 't Hof committed
93
94
95
96
97
98
    } text ("Given sample must have 1 alternative allele")
    opt[String]("diffGenotype") unbounded () valueName ("<sample:sample>") action { (x, c) =>
      c.copy(diffGenotype = (x.split(":")(0), x.split(":")(1)) :: c.diffGenotype)
    } validate { x => if (x.split(":").length == 2) success else failure("--notSameGenotype should be in this format: sample:sample")
    } text ("Given samples must have a different genotype")
    opt[String]("filterHetVarToHomVar") unbounded () valueName ("<sample:sample>") action { (x, c) =>
99
      c.copy(filterHetVarToHomVar = (x.split(":")(0), x.split(":")(1)) :: c.filterHetVarToHomVar)
Peter van 't Hof's avatar
Peter van 't Hof committed
100
101
    } validate { x => if (x.split(":").length == 2) success else failure("--filterHetVarToHomVar should be in this format: sample:sample")
    } text ("If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filterd")
Peter van 't Hof's avatar
Peter van 't Hof committed
102
103
    opt[Unit]("filterRefCalls") unbounded () action { (x, c) =>
      c.copy(filterRefCalls = true)
Peter van 't Hof's avatar
Peter van 't Hof committed
104
    } text ("Filter when there are only ref calls")
105
106
107
    opt[Unit]("filterNoCalls") unbounded () action { (x, c) =>
      c.copy(filterNoCalls = true)
    } text ("Filter when there are only no calls")
Peter van 't Hof's avatar
Peter van 't Hof committed
108
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
109

110
111
  var commandArgs: Args = _

Peter van 't Hof's avatar
Peter van 't Hof committed
112
113
114
115
  /**
   * @param args the command line arguments
   */
  def main(args: Array[String]): Unit = {
Peter van 't Hof's avatar
Peter van 't Hof committed
116
    val argsParser = new OptParser
117
    commandArgs = argsParser.parse(args, Args()) getOrElse sys.exit(1)
Peter van 't Hof's avatar
Peter van 't Hof committed
118

Peter van 't Hof's avatar
Peter van 't Hof committed
119
    val reader = new VCFFileReader(commandArgs.inputVcf, false)
Peter van 't Hof's avatar
Peter van 't Hof committed
120
    val header = reader.getFileHeader
Peter van 't Hof's avatar
Peter van 't Hof committed
121
    val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().setOutputFile(commandArgs.outputVcf).build)
Peter van 't Hof's avatar
Peter van 't Hof committed
122
    writer.writeHeader(header)
Peter van 't Hof's avatar
Peter van 't Hof committed
123

Peter van 't Hof's avatar
Peter van 't Hof committed
124
    for (record <- reader) {
125
126
127
128
129
      if (filterRefCalls(record) &&
        filterNoCalls(record) &&
        minTotalDepth(record) &&
        minSampleDepth(record) &&
        minAlternateDepth(record) &&
130
131
132
133
        minBamAlternateDepth(record, header) &&
        mustHaveVariant(record) &&
        notSameGenotype(record) &&
        filterHetVarToHomVar(record) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
134
        denovoInSample(record)) {
Peter van 't Hof's avatar
Peter van 't Hof committed
135
        writer.add(record)
Peter van 't Hof's avatar
Peter van 't Hof committed
136
      }
Peter van 't Hof's avatar
Peter van 't Hof committed
137
138
139
140
    }
    reader.close
    writer.close
  }
141

142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
  def filterRefCalls(record: VariantContext): Boolean = {
    if (commandArgs.filterNoCalls) record.getGenotypes.exists(g => !g.isHomRef)
    else true
  }

  def filterNoCalls(record: VariantContext): Boolean = {
    if (commandArgs.filterNoCalls) record.getGenotypes.exists(g => !g.isNoCall)
    else true
  }

  def minTotalDepth(record: VariantContext): Boolean = {
    record.getAttributeAsInt("DP", -1) >= commandArgs.minTotalDepth
  }

  def minSampleDepth(record: VariantContext): Boolean = {
    record.getGenotypes.count(genotype => {
      val DP = if (genotype.hasDP) genotype.getDP else -1
      DP >= commandArgs.minSampleDepth
    }) >= commandArgs.minSamplesPass
  }

  def minAlternateDepth(record: VariantContext): Boolean = {
    record.getGenotypes.count(genotype => {
      val AD = if (genotype.hasAD) List(genotype.getAD: _*) else Nil
      if (!AD.isEmpty) AD.tail.count(_ >= commandArgs.minAlternateDepth) > 0 else true
    }) >= commandArgs.minSamplesPass
  }

170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
  def minBamAlternateDepth(record: VariantContext, header: VCFHeader): Boolean = {
    val bamADFields = (for (line <- header.getInfoHeaderLines if line.getID.startsWith("BAM-AD-")) yield line.getID).toList

    val bamADvalues = (for (field <- bamADFields) yield {
      record.getAttribute(field, new ArrayList) match {
        case t: ArrayList[_] if t.length > 1 => {
          for (i <- 1 until t.size) yield {
            t(i) match {
              case a: Int    => a > commandArgs.minBamAlternateDepth
              case a: String => a.toInt > commandArgs.minBamAlternateDepth
              case _         => false
            }
          }
        }
        case _ => List(false)
      }
    }).flatten

    return commandArgs.minBamAlternateDepth <= 0 || bamADvalues.count(_ == true) >= commandArgs.minSamplesPass
  }

  def mustHaveVariant(record: VariantContext): Boolean = {
    return !commandArgs.mustHaveVariant.map(record.getGenotype(_)).exists(a => a.isHomRef || a.isNoCall)
  }

  def notSameGenotype(record: VariantContext): Boolean = {
Peter van 't Hof's avatar
Peter van 't Hof committed
196
    for ((sample1, sample2) <- commandArgs.diffGenotype) {
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
      val genotype1 = record.getGenotype(sample1)
      val genotype2 = record.getGenotype(sample2)
      if (genotype1.sameGenotype(genotype2)) return false
    }
    return true
  }

  def filterHetVarToHomVar(record: VariantContext): Boolean = {
    for ((sample1, sample2) <- commandArgs.filterHetVarToHomVar) {
      val genotype1 = record.getGenotype(sample1)
      val genotype2 = record.getGenotype(sample2)
      if (genotype1.isHet && !genotype1.getAlleles.forall(_.isNonReference)) {
        for (allele <- genotype1.getAlleles if allele.isNonReference) {
          if (genotype2.getAlleles.forall(_.basesMatch(allele))) return false
        }
      }
    }
    return true
  }

  def denovoInSample(record: VariantContext): Boolean = {
    if (commandArgs.denovoInSample == null) return true
    val genotype = record.getGenotype(commandArgs.denovoInSample)
    for (allele <- genotype.getAlleles if allele.isNonReference) {
      for (g <- record.getGenotypes if g.getSampleName != commandArgs.denovoInSample) {
        if (g.getAlleles.exists(_.basesMatch(allele))) return false
      }
    }
    return true
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
227
}