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Merge pull request #65 from broadinstitute/dr_change_haplotypecaller_…

…downsampling_settings_GSA-699

Change default downsampling coverage target for the HaplotypeCaller to 2...
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commit 357a05683d773723377e5fb9db0361ea6633d455 2 parents 51d618d + 8b29030
Ryan Poplin rpoplin authored
2  protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -133,7 +133,7 @@
133 133 @PartitionBy(PartitionType.LOCUS)
134 134 @BAQMode(ApplicationTime = ReadTransformer.ApplicationTime.FORBIDDEN)
135 135 @ActiveRegionTraversalParameters(extension=85, maxRegion=300)
136   -@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=30)
  136 +@Downsample(by= DownsampleType.BY_SAMPLE, toCoverage=250)
137 137 public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implements AnnotatorCompatible {
138 138
139 139 /**
8 protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/BiasedDownsamplingIntegrationTest.java
@@ -255,7 +255,7 @@ public void testHCContaminationDownsamplingFlat() {
255 255 final String baseCommand = "-T HaplotypeCaller -R " + b36KGReference + " --no_cmdline_in_header --dbsnp " + b36dbSNP129;
256 256 WalkerTestSpec spec = new WalkerTestSpec(
257 257 baseCommand + " -I " + validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SLX.bam -o %s -L 1:10,000,000-10,010,000 -contamination 0.20", 1,
258   - Arrays.asList("3a66513cdfef46f315d5ada8a104822f"));
  258 + Arrays.asList("c3a253467ead7b1cfe9fd9dd310828b1"));
259 259 executeTest("HC calling with contamination_percentage_to_filter 0.20", spec);
260 260 }
261 261
@@ -283,17 +283,17 @@ private void testHCFlatContamination(final String bam1, final String bam2, final
283 283
284 284 @Test
285 285 public void testHCFlatContaminationCase1() {
286   - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "9dbd17769e091ce759efda050cd4f8b2");
  286 + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.05, "c3e695381d8627e3922d8c642b66c3ce");
287 287 }
288 288
289 289 @Test
290 290 public void testHCFlatContaminationCase2() {
291   - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "b8cee98c9c693fd336fc5e574dd744ed");
  291 + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.1, "002d2b45336d88d7c04e19f9f26e29d9");
292 292 }
293 293
294 294 @Test
295 295 public void testHCFlatContaminationCase3() {
296   - testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "e7309bd594b8e4b54b712f9877518b8e");
  296 + testHCFlatContamination("NA11918.with.1.NA12842.reduced.bam", "NA12842.with.1.NA11918.reduced.bam", 0.2, "1809a33ac112d1a3bd7a071c566794dd");
297 297 }
298 298
299 299 }
18 ...cted/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCallerIntegrationTest.java
@@ -68,12 +68,12 @@ private void HCTest(String bam, String args, String md5) {
68 68
69 69 @Test
70 70 public void testHaplotypeCallerMultiSample() {
71   - HCTest(CEUTRIO_BAM, "", "a9748a39604c4ec8bbdb2cb809a971f1");
  71 + HCTest(CEUTRIO_BAM, "", "aac5517a0a64ad291b6b00825d982f7f");
72 72 }
73 73
74 74 @Test
75 75 public void testHaplotypeCallerSingleSample() {
76   - HCTest(NA12878_BAM, "", "c55ebed976767e1f93d2e8ada9d52bf8");
  76 + HCTest(NA12878_BAM, "", "3bfab723fb0f3a65998d82152b67ed15");
77 77 }
78 78
79 79 @Test(enabled = false)
@@ -84,7 +84,7 @@ public void testHaplotypeCallerSingleSampleWithDbsnp() {
84 84 @Test
85 85 public void testHaplotypeCallerMultiSampleGGA() {
86 86 HCTest(CEUTRIO_BAM, "--max_alternate_alleles 3 -gt_mode GENOTYPE_GIVEN_ALLELES -out_mode EMIT_ALL_SITES -alleles " + validationDataLocation + "combined.phase1.chr20.raw.indels.sites.vcf",
87   - "70a53e566e6a7090e2f29ed608e9d84f");
  87 + "283524b3e3397634d4cf0dc2b8723002");
88 88 }
89 89
90 90 private void HCTestComplexGGA(String bam, String args, String md5) {
@@ -96,13 +96,13 @@ private void HCTestComplexGGA(String bam, String args, String md5) {
96 96 @Test
97 97 public void testHaplotypeCallerMultiSampleGGAComplex() {
98 98 HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:119673-119823 -L 20:121408-121538",
99   - "1d9cd5017e420d5862b7b94e6cb5de3b");
  99 + "417174e043dbb8b86cc3871da9b50536");
100 100 }
101 101
102 102 @Test
103 103 public void testHaplotypeCallerMultiSampleGGAMultiAllelic() {
104 104 HCTestComplexGGA(NA12878_CHR20_BAM, "-L 20:133041-133161 -L 20:300207-300337",
105   - "10fdbfeb3b4ea1af7f242a8aca83cb9b");
  105 + "f2df7a8f53ce449e4a8e8f8496e7c745");
106 106 }
107 107
108 108 private void HCTestComplexVariants(String bam, String args, String md5) {
@@ -125,7 +125,7 @@ private void HCTestSymbolicVariants(String bam, String args, String md5) {
125 125 // TODO -- need a better symbolic allele test
126 126 @Test
127 127 public void testHaplotypeCallerSingleSampleSymbolic() {
128   - HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "f893aa7afef71705df7f040b22440a2d");
  128 + HCTestSymbolicVariants(NA12878_CHR20_BAM, "", "56f2ef9acc6c0d267cf2b7a447d87fb7");
129 129 }
130 130
131 131 private void HCTestIndelQualityScores(String bam, String args, String md5) {
@@ -146,7 +146,7 @@ public void testHaplotypeCallerSingleSampleIndelQualityScores() {
146 146 @Test
147 147 public void HCTestProblematicReadsModifiedInActiveRegions() {
148 148 final String base = String.format("-T HaplotypeCaller -R %s -I %s", REF, privateTestDir + "haplotype-problem-4.bam") + " --no_cmdline_in_header -o %s -minPruning 3 -L 4:49139026-49139965";
149   - final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("0689d2c202849fd05617648eaf429b9a"));
  149 + final WalkerTestSpec spec = new WalkerTestSpec(base, Arrays.asList("ccd30e226f097a40cdeebaa035a290a7"));
150 150 executeTest("HCTestProblematicReadsModifiedInActiveRegions: ", spec);
151 151 }
152 152
@@ -175,7 +175,7 @@ public void HCTestDoesNotFailOnBadRefBase() {
175 175 public void HCTestReducedBam() {
176 176 WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
177 177 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "bamExample.ReducedRead.ADAnnotation.bam -o %s -L 1:67,225,396-67,288,518", 1,
178   - Arrays.asList("2ab038f4f6c262b3245b6fa549659c5e"));
  178 + Arrays.asList("adb08cb25e902cfe0129404a682b2169"));
179 179 executeTest("HC calling on a ReducedRead BAM", spec);
180 180 }
181 181
@@ -183,7 +183,7 @@ public void HCTestReducedBam() {
183 183 public void testReducedBamWithReadsNotFullySpanningDeletion() {
184 184 WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
185 185 "-T HaplotypeCaller -R " + b37KGReference + " --no_cmdline_in_header -I " + privateTestDir + "reduced.readNotFullySpanningDeletion.bam -o %s -L 1:167871297", 1,
186   - Arrays.asList("56fc9110974bfa9c9fe196b0d4af4e64"));
  186 + Arrays.asList("6debe567cd5ed7eb5756b6605a151f56"));
187 187 executeTest("test calling on a ReducedRead BAM where the reads do not fully span a deletion", spec);
188 188 }
189 189 }

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