VcfFilter.scala 17.8 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
Peter van 't Hof's avatar
Peter van 't Hof committed
16
package nl.lumc.sasc.biopet.tools
Peter van 't Hof's avatar
Peter van 't Hof committed
17
18

import java.io.File
Peter van 't Hof's avatar
Peter van 't Hof committed
19

20
import htsjdk.variant.variantcontext.{ GenotypeType, VariantContext }
Peter van 't Hof's avatar
Peter van 't Hof committed
21
22
import htsjdk.variant.variantcontext.writer.{ AsyncVariantContextWriter, VariantContextWriterBuilder }
import htsjdk.variant.vcf.VCFFileReader
Peter van 't Hof's avatar
Peter van 't Hof committed
23
import nl.lumc.sasc.biopet.utils.ToolCommand
Peter van 't Hof's avatar
Peter van 't Hof committed
24

Peter van 't Hof's avatar
Peter van 't Hof committed
25
import scala.collection.JavaConversions._
26
import scala.io.Source
Peter van 't Hof's avatar
Peter van 't Hof committed
27

Peter van 't Hof's avatar
Peter van 't Hof committed
28
object VcfFilter extends ToolCommand {
Peter van 't Hof's avatar
Peter van 't Hof committed
29
  /** Container class for a trio */
Sander Bollen's avatar
Sander Bollen committed
30
  protected[tools] case class Trio(child: String, father: String, mother: String) {
Peter van 't Hof's avatar
Peter van 't Hof committed
31
32
33
34
35
    def this(arg: String) = {
      this(arg.split(":")(0), arg.split(":")(1), arg.split(":")(2))
    }
  }

36
37
  case class Args(inputVcf: File = null,
                  outputVcf: File = null,
Peter van 't Hof's avatar
Peter van 't Hof committed
38
                  invertedOutputVcf: Option[File] = None,
39
                  minQualScore: Option[Double] = None,
40
41
42
                  minSampleDepth: Int = -1,
                  minTotalDepth: Int = -1,
                  minAlternateDepth: Int = -1,
Peter van 't Hof's avatar
Peter van 't Hof committed
43
                  minSamplesPass: Int = 1,
44
                  mustHaveVariant: List[String] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
45
                  calledIn: List[String] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
46
                  mustHaveGenotype: List[(String, GenotypeType)] = Nil,
47
                  deNovoInSample: String = null,
Peter van 't Hof's avatar
Peter van 't Hof committed
48
                  resToDom: List[Trio] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
49
                  trioCompound: List[Trio] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
50
51
                  deNovoTrio: List[Trio] = Nil,
                  trioLossOfHet: List[Trio] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
52
                  diffGenotype: List[(String, String)] = Nil,
53
                  filterHetVarToHomVar: List[(String, String)] = Nil,
Peter van 't Hof's avatar
Peter van 't Hof committed
54
55
                  uniqueOnly: Boolean = false,
                  sharedOnly: Boolean = false,
56
                  filterRefCalls: Boolean = false,
57
                  filterNoCalls: Boolean = false,
58
59
                  iDset: Set[String] = Set(),
                  minGenomeQuality: Int = 0) extends AbstractArgs
Peter van 't Hof's avatar
Peter van 't Hof committed
60
61

  class OptParser extends AbstractOptParser {
Peter van 't Hof's avatar
Peter van 't Hof committed
62
    opt[File]('I', "inputVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
63
      c.copy(inputVcf = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
64
65
    } text "Input vcf file"
    opt[File]('o', "outputVcf") required () maxOccurs 1 valueName "<file>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
66
      c.copy(outputVcf = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
67
68
    } text "Output vcf file"
    opt[File]("invertedOutputVcf") maxOccurs 1 valueName "<file>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
69
      c.copy(invertedOutputVcf = Some(x))
Peter van 't Hof's avatar
Peter van 't Hof committed
70
71
    } text "inverted output vcf file"
    opt[Int]("minSampleDepth") unbounded () valueName "<int>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
72
      c.copy(minSampleDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
73
74
    } 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
75
      c.copy(minTotalDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
76
77
    } 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
78
      c.copy(minAlternateDepth = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
79
80
    } 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
81
      c.copy(minSamplesPass = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
82
83
    } text "Min number off samples to pass --minAlternateDepth, --minBamAlternateDepth and --minSampleDepth"
    opt[String]("resToDom") unbounded () valueName "<child:father:mother>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
84
      c.copy(resToDom = new Trio(x) :: c.resToDom)
Peter van 't Hof's avatar
Peter van 't Hof committed
85
86
    } text "Only shows variants where child is homozygous and both parants hetrozygous"
    opt[String]("trioCompound") unbounded () valueName "<child:father:mother>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
87
      c.copy(trioCompound = new Trio(x) :: c.trioCompound)
Peter van 't Hof's avatar
Peter van 't Hof committed
88
89
    } text "Only shows variants where child is a compound variant combined from both parants"
    opt[String]("deNovoInSample") maxOccurs 1 unbounded () valueName "<sample>" action { (x, c) =>
90
      c.copy(deNovoInSample = x)
Peter van 't Hof's avatar
Peter van 't Hof committed
91
92
    } text "Only show variants that contain unique alleles in complete set for given sample"
    opt[String]("deNovoTrio") unbounded () valueName "<child:father:mother>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
93
      c.copy(deNovoTrio = new Trio(x) :: c.deNovoTrio)
Peter van 't Hof's avatar
Peter van 't Hof committed
94
95
    } text "Only show variants that are denovo in the trio"
    opt[String]("trioLossOfHet") unbounded () valueName "<child:father:mother>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
96
      c.copy(trioLossOfHet = new Trio(x) :: c.trioLossOfHet)
Peter van 't Hof's avatar
Peter van 't Hof committed
97
98
    } text "Only show variants where a loss of hetrozygosity is detected"
    opt[String]("mustHaveVariant") unbounded () valueName "<sample>" action { (x, c) =>
99
      c.copy(mustHaveVariant = x :: c.mustHaveVariant)
Peter van 't Hof's avatar
Peter van 't Hof committed
100
101
    } text "Given sample must have 1 alternative allele"
    opt[String]("calledIn") unbounded () valueName "<sample>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
102
      c.copy(calledIn = x :: c.calledIn)
Peter van 't Hof's avatar
Peter van 't Hof committed
103
    } text "Must be called in this sample"
104
    opt[String]("mustHaveGenotype") unbounded () valueName "<sample:genotype>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
105
106
      c.copy(mustHaveGenotype = (x.split(":")(0), GenotypeType.valueOf(x.split(":")(1))) :: c.mustHaveGenotype)
    } validate { x =>
Sander Bollen's avatar
Sander Bollen committed
107
      if (x.split(":").length == 2 && GenotypeType.values().map(_.toString).contains(x.split(":")(1))) success
Peter van 't Hof's avatar
Peter van 't Hof committed
108
109
      else failure("--mustHaveGenotype should be in this format: sample:genotype")
    } text "Must have genotoype <genotype> for this sample. Genotype can be " + GenotypeType.values().mkString(", ")
Peter van 't Hof's avatar
Peter van 't Hof committed
110
    opt[String]("diffGenotype") unbounded () valueName "<sample:sample>" action { (x, c) =>
Peter van 't Hof's avatar
Peter van 't Hof committed
111
112
      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")
Peter van 't Hof's avatar
Peter van 't Hof committed
113
114
    } text "Given samples must have a different genotype"
    opt[String]("filterHetVarToHomVar") unbounded () valueName "<sample:sample>" action { (x, c) =>
115
      c.copy(filterHetVarToHomVar = (x.split(":")(0), x.split(":")(1)) :: c.filterHetVarToHomVar)
Peter van 't Hof's avatar
Peter van 't Hof committed
116
    } validate { x => if (x.split(":").length == 2) success else failure("--filterHetVarToHomVar should be in this format: sample:sample")
Peter van 't Hof's avatar
Peter van 't Hof committed
117
    } text "If variants in sample 1 are heterogeneous and alternative alleles are homogeneous in sample 2 variants are filtered"
Peter van 't Hof's avatar
Peter van 't Hof committed
118
119
    opt[Unit]("filterRefCalls") unbounded () action { (x, c) =>
      c.copy(filterRefCalls = true)
Peter van 't Hof's avatar
Peter van 't Hof committed
120
    } text "Filter when there are only ref calls"
121
122
    opt[Unit]("filterNoCalls") unbounded () action { (x, c) =>
      c.copy(filterNoCalls = true)
Peter van 't Hof's avatar
Peter van 't Hof committed
123
    } text "Filter when there are only no calls"
Peter van 't Hof's avatar
Peter van 't Hof committed
124
125
126
127
128
129
    opt[Unit]("uniqueOnly") unbounded () action { (x, c) =>
      c.copy(uniqueOnly = true)
    } text "Filter when there more then 1 sample have this variant"
    opt[Unit]("sharedOnly") unbounded () action { (x, c) =>
      c.copy(sharedOnly = true)
    } text "Filter when not all samples have this variant"
130
131
    opt[Double]("minQualScore") unbounded () action { (x, c) =>
      c.copy(minQualScore = Some(x))
Peter van 't Hof's avatar
Peter van 't Hof committed
132
    } text "Min qual score"
133
134
    opt[String]("id") unbounded () action { (x, c) =>
      c.copy(iDset = c.iDset + x)
Peter van 't Hof's avatar
Peter van 't Hof committed
135
    } text "Id that may pass the filter"
136
    opt[File]("idFile") unbounded () action { (x, c) =>
137
      c.copy(iDset = c.iDset ++ Source.fromFile(x).getLines())
Peter van 't Hof's avatar
Peter van 't Hof committed
138
    } text "File that contain list of IDs to get from vcf file"
Sander Bollen's avatar
Sander Bollen committed
139
140
141
    opt[Int]("minGenomeQuality") unbounded () action { (x, c) =>
      c.copy(minGenomeQuality = x)
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
142
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
143

Peter van 't Hof's avatar
Peter van 't Hof committed
144
  /** @param args the command line arguments */
Peter van 't Hof's avatar
Peter van 't Hof committed
145
  def main(args: Array[String]): Unit = {
146
    logger.info("Start")
Peter van 't Hof's avatar
Peter van 't Hof committed
147
    val argsParser = new OptParser
Peter van 't Hof's avatar
Peter van 't Hof committed
148
    val cmdArgs = argsParser.parse(args, Args()) getOrElse (throw new IllegalArgumentException)
Peter van 't Hof's avatar
Peter van 't Hof committed
149

Peter van 't Hof's avatar
Peter van 't Hof committed
150
    val reader = new VCFFileReader(cmdArgs.inputVcf, false)
Peter van 't Hof's avatar
Peter van 't Hof committed
151
    val header = reader.getFileHeader
152
    val writer = new AsyncVariantContextWriter(new VariantContextWriterBuilder().
Peter van 't Hof's avatar
Peter van 't Hof committed
153
      setOutputFile(cmdArgs.outputVcf).
154
155
      setReferenceDictionary(header.getSequenceDictionary).
      build)
Peter van 't Hof's avatar
Peter van 't Hof committed
156
    writer.writeHeader(header)
Peter van 't Hof's avatar
Peter van 't Hof committed
157

Peter van 't Hof's avatar
Peter van 't Hof committed
158
    val invertedWriter = cmdArgs.invertedOutputVcf.collect {
Sander Bollen's avatar
Sander Bollen committed
159
160
161
162
163
      case x => new VariantContextWriterBuilder().
        setOutputFile(x).
        setReferenceDictionary(header.getSequenceDictionary).
        build
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
164
    invertedWriter.foreach(_.writeHeader(header))
Peter van 't Hof's avatar
Peter van 't Hof committed
165

166
167
    var counterTotal = 0
    var counterLeft = 0
Peter van 't Hof's avatar
Peter van 't Hof committed
168
    for (record <- reader) {
Peter van 't Hof's avatar
Peter van 't Hof committed
169
170
171
      if (cmdArgs.minQualScore.map(minQualscore(record, _)).getOrElse(true) &&
        (!cmdArgs.filterRefCalls || hasNonRefCalls(record)) &&
        (!cmdArgs.filterNoCalls || hasCalls(record)) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
172
173
        (!cmdArgs.uniqueOnly || hasUniqeSample(record)) &&
        (!cmdArgs.sharedOnly || allSamplesVariant(record)) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
174
175
176
        hasMinTotalDepth(record, cmdArgs.minTotalDepth) &&
        hasMinSampleDepth(record, cmdArgs.minSampleDepth, cmdArgs.minSamplesPass) &&
        minAlternateDepth(record, cmdArgs.minAlternateDepth, cmdArgs.minSamplesPass) &&
177
        minGenomeQuality(record, cmdArgs.minGenomeQuality, cmdArgs.minSamplesPass) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
178
        (cmdArgs.mustHaveVariant.isEmpty || mustHaveVariant(record, cmdArgs.mustHaveVariant)) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
179
180
        calledIn(record, cmdArgs.calledIn) &&
        hasGenotype(record, cmdArgs.mustHaveGenotype) &&
Peter van 't Hof's avatar
Peter van 't Hof committed
181
182
183
184
185
186
187
188
189
190
191
        (cmdArgs.diffGenotype.isEmpty || cmdArgs.diffGenotype.forall(x => notSameGenotype(record, x._1, x._2))) &&
        (
          cmdArgs.filterHetVarToHomVar.isEmpty ||
          cmdArgs.filterHetVarToHomVar.forall(x => filterHetVarToHomVar(record, x._1, x._2))
        ) &&
          denovoInSample(record, cmdArgs.deNovoInSample) &&
          denovoTrio(record, cmdArgs.deNovoTrio) &&
          denovoTrio(record, cmdArgs.trioLossOfHet, onlyLossHet = true) &&
          resToDom(record, cmdArgs.resToDom) &&
          trioCompound(record, cmdArgs.trioCompound) &&
          (cmdArgs.iDset.isEmpty || inIdSet(record, cmdArgs.iDset))) {
Peter van 't Hof's avatar
Peter van 't Hof committed
192
        writer.add(record)
193
        counterLeft += 1
Peter van 't Hof's avatar
Peter van 't Hof committed
194
195
      } else
        invertedWriter.foreach(_.add(record))
196
      counterTotal += 1
Peter van 't Hof's avatar
Peter van 't Hof committed
197
      if (counterTotal % 100000 == 0) logger.info(s"$counterTotal variants processed, $counterLeft passed filter")
Peter van 't Hof's avatar
Peter van 't Hof committed
198
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
199
    logger.info(s"$counterTotal variants processed, $counterLeft passed filter")
Peter van 't Hof's avatar
Peter van 't Hof committed
200
201
    reader.close()
    writer.close()
Peter van 't Hof's avatar
Peter van 't Hof committed
202
    invertedWriter.foreach(_.close())
203
    logger.info("Done")
Peter van 't Hof's avatar
Peter van 't Hof committed
204
  }
205

Peter van 't Hof's avatar
Peter van 't Hof committed
206
207
208
209
210
211
212
213
  /**
   * Checks if given samples are called
   * @param record VCF record
   * @param samples Samples that need this sample to be called
   * @return false when filters fail
   */
  def calledIn(record: VariantContext, samples: List[String]): Boolean = {
    if (!samples.forall(record.getGenotype(_).isCalled)) false
Peter van 't Hof's avatar
Peter van 't Hof committed
214
215
216
    else true
  }

217
218
219
220
221
222
  /**
   * Checks if given genotypes for given samples are there
   * @param record VCF record
   * @param samplesGenotypes samples and their associated genotypes to be checked (of format sample:genotype)
   * @return false when filter fails
   */
Peter van 't Hof's avatar
Peter van 't Hof committed
223
224
  def hasGenotype(record: VariantContext, samplesGenotypes: List[(String, GenotypeType)]): Boolean = {
    samplesGenotypes.forall(x => record.getGenotype(x._1).getType == x._2)
225
226
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
227
228
229
230
231
232
233
234
  /**
   * Checks if record has atleast minQualScore
   * @param record VCF record
   * @param minQualScore Minimal quality score
   * @return false when filters fail
   */
  def minQualscore(record: VariantContext, minQualScore: Double): Boolean = {
    record.getPhredScaledQual >= minQualScore
Peter van 't Hof's avatar
Peter van 't Hof committed
235
236
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
237
  /** returns true record contains Non reference genotypes */
Peter van 't Hof's avatar
Peter van 't Hof committed
238
239
  def hasNonRefCalls(record: VariantContext): Boolean = {
    record.getGenotypes.exists(g => !g.isHomRef)
240
241
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
242
  /** returns true when record has calls */
Peter van 't Hof's avatar
Peter van 't Hof committed
243
244
  def hasCalls(record: VariantContext): Boolean = {
    record.getGenotypes.exists(g => !g.isNoCall)
245
246
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
247
248
249
250
251
252
253
254
255
256
  /** Checks if there is a variant in only 1 sample */
  def hasUniqeSample(record: VariantContext): Boolean = {
    record.getGenotypes.count(_.getAlleles.exists(a => a.isNonReference && !a.isNoCall)) == 1
  }

  /** Checks if all samples are a variant */
  def allSamplesVariant(record: VariantContext): Boolean = {
    record.getGenotypes.forall(_.getAlleles.exists(a => a.isNonReference && !a.isNoCall))
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
257
  /** returns true when DP INFO field is atleast the given value */
Peter van 't Hof's avatar
Peter van 't Hof committed
258
259
  def hasMinTotalDepth(record: VariantContext, minTotalDepth: Int): Boolean = {
    record.getAttributeAsInt("DP", -1) >= minTotalDepth
260
261
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
262
263
264
265
266
267
268
269
  /**
   * Checks if DP genotype field have a minimal value
   * @param record VCF record
   * @param minSampleDepth minimal depth
   * @param minSamplesPass Minimal number of samples to pass filter
   * @return true if filter passed
   */
  def hasMinSampleDepth(record: VariantContext, minSampleDepth: Int, minSamplesPass: Int = 1): Boolean = {
270
271
    record.getGenotypes.count(genotype => {
      val DP = if (genotype.hasDP) genotype.getDP else -1
Peter van 't Hof's avatar
Peter van 't Hof committed
272
273
      DP >= minSampleDepth
    }) >= minSamplesPass
274
275
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
276
  /**
277
   * Checks if non-ref AD genotype field have a minimal value
Peter van 't Hof's avatar
Peter van 't Hof committed
278
279
280
281
282
283
   * @param record VCF record
   * @param minAlternateDepth minimal depth
   * @param minSamplesPass Minimal number of samples to pass filter
   * @return true if filter passed
   */
  def minAlternateDepth(record: VariantContext, minAlternateDepth: Int, minSamplesPass: Int = 1): Boolean = {
284
285
    record.getGenotypes.count(genotype => {
      val AD = if (genotype.hasAD) List(genotype.getAD: _*) else Nil
Peter van 't Hof's avatar
Peter van 't Hof committed
286
      if (AD.nonEmpty && minAlternateDepth >= 0) AD.tail.count(_ >= minAlternateDepth) > 0 else true
Peter van 't Hof's avatar
Peter van 't Hof committed
287
    }) >= minSamplesPass
288
289
  }

290
291
292
293
294
295
296
297
  /**
   * Checks if genome quality field has minimum value
   * @param record VCF record
   * @param minGQ smallest GQ allowed
   * @param minSamplesPass number of samples to consider
   * @return
   */
  def minGenomeQuality(record: VariantContext, minGQ: Int, minSamplesPass: Int = 1): Boolean = {
Peter van 't Hof's avatar
Peter van 't Hof committed
298
299
300
301
    record.getGenotypes.count(x =>
      if (minGQ == 0) true
      else if (!x.hasGQ) false
      else if (x.getGQ >= minGQ) true else false) >= minSamplesPass
302
303
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
304
305
306
307
308
309
  /**
   * Checks if given samples does have a variant hin this record
   * @param record VCF record
   * @param mustHaveVariant List of samples that should have this variant
   * @return true if filter passed
   */
Peter van 't Hof's avatar
Peter van 't Hof committed
310
311
  def mustHaveVariant(record: VariantContext, mustHaveVariant: List[String]): Boolean = {
    !mustHaveVariant.map(record.getGenotype).exists(a => a.isHomRef || a.isNoCall)
312
313
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
314
  /** Checks if given samples have the same genotype */
Peter van 't Hof's avatar
Peter van 't Hof committed
315
316
317
318
319
  def notSameGenotype(record: VariantContext, sample1: String, sample2: String): Boolean = {
    val genotype1 = record.getGenotype(sample1)
    val genotype2 = record.getGenotype(sample2)
    if (genotype1.sameGenotype(genotype2)) false
    else true
320
321
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
322
  /** Checks if sample1 is hetrozygous and if sample2 is homozygous for a alternative allele in sample1 */
Peter van 't Hof's avatar
Peter van 't Hof committed
323
324
325
326
327
328
  def filterHetVarToHomVar(record: VariantContext, sample1: String, sample2: String): Boolean = {
    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
329
330
      }
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
331
    true
332
333
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
334
  /** Checks if given sample have alternative alleles that are unique in the VCF record */
Peter van 't Hof's avatar
Peter van 't Hof committed
335
336
337
338
339
340
  def denovoInSample(record: VariantContext, sample: String): Boolean = {
    if (sample == null) return true
    val genotype = record.getGenotype(sample)
    if (genotype.isNoCall) return false
    for (allele <- genotype.getAlleles) {
      for (g <- record.getGenotypes if g.getSampleName != sample) {
341
342
343
        if (g.getAlleles.exists(_.basesMatch(allele))) return false
      }
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
344
    true
345
  }
346

Peter van 't Hof's avatar
Peter van 't Hof committed
347
  /** Return true when variant is homozygous in the child and hetrozygous in parants */
Peter van 't Hof's avatar
Peter van 't Hof committed
348
349
350
351
352
353
354
355
356
  def resToDom(record: VariantContext, trios: List[Trio]): Boolean = {
    for (trio <- trios) {
      val child = record.getGenotype(trio.child)

      if (child.isHomVar && child.getAlleles.forall(allele => {
        record.getGenotype(trio.father).countAllele(allele) == 1 &&
          record.getGenotype(trio.mother).countAllele(allele) == 1
      })) return true
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
357
    trios.isEmpty
Peter van 't Hof's avatar
Peter van 't Hof committed
358
359
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
360
  /** Returns true when variant a compound variant in the child and hetrozygous in parants */
Peter van 't Hof's avatar
Peter van 't Hof committed
361
362
363
364
365
366
367
368
369
  def trioCompound(record: VariantContext, trios: List[Trio]): Boolean = {
    for (trio <- trios) {
      val child = record.getGenotype(trio.child)

      if (child.isHetNonRef && child.getAlleles.forall(allele => {
        record.getGenotype(trio.father).countAllele(allele) >= 1 &&
          record.getGenotype(trio.mother).countAllele(allele) >= 1
      })) return true
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
370
    trios.isEmpty
Peter van 't Hof's avatar
Peter van 't Hof committed
371
372
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
373
  /** Returns true when child got a deNovo variant */
Peter van 't Hof's avatar
Peter van 't Hof committed
374
375
376
377
378
379
380
381
382
383
384
  def denovoTrio(record: VariantContext, trios: List[Trio], onlyLossHet: Boolean = false): Boolean = {
    for (trio <- trios) {
      val child = record.getGenotype(trio.child)
      val father = record.getGenotype(trio.father)
      val mother = record.getGenotype(trio.mother)

      for (allele <- child.getAlleles) {
        val childCount = child.countAllele(allele)
        val fatherCount = father.countAllele(allele)
        val motherCount = mother.countAllele(allele)

Peter van 't Hof's avatar
Peter van 't Hof committed
385
386
387
388
389
390
391
392
        if (onlyLossHet) {
          if (childCount == 2 && (
            (fatherCount == 2 && motherCount == 0) ||
            (fatherCount == 0 && motherCount == 2))) return true
        } else {
          if (childCount == 1 && fatherCount == 0 && motherCount == 0) return true
          else if (childCount == 2 && (fatherCount == 0 || motherCount == 0)) return true
        }
Peter van 't Hof's avatar
Peter van 't Hof committed
393
394
      }
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
395
    trios.isEmpty
Peter van 't Hof's avatar
Peter van 't Hof committed
396
397
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
398
  /** Returns true when VCF record contains a ID from the given list */
Peter van 't Hof's avatar
Peter van 't Hof committed
399
400
  def inIdSet(record: VariantContext, idSet: Set[String]): Boolean = {
    record.getID.split(",").exists(idSet.contains)
401
  }
Peter van 't Hof's avatar
Peter van 't Hof committed
402
}