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Contig Ploidy warnings with GermlineCNVCaller

TintestTintest FranceMember
edited October 2018 in Ask the GATK team

Hello,

I'm currently working with an infertile exome cohort and I might have some chromosomal abnormalities like Klinefelter Syndromes in my datasets.

I got those errors while running GermlineCNVCaller 4.0.10.0-0 :

 06:00:35.093 WARNING gcnvkernel.structs.metadata - Sample grexome0078 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.103 WARNING gcnvkernel.structs.metadata - Sample grexome0406 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.113 WARNING gcnvkernel.structs.metadata - Sample grexome0128 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.121 WARNING gcnvkernel.structs.metadata - Sample grexome0218 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.131 WARNING gcnvkernel.structs.metadata - Sample grexome0085 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.142 WARNING gcnvkernel.structs.metadata - Sample grexome0420 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.156 WARNING gcnvkernel.structs.metadata - Sample grexome0227 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.168 WARNING gcnvkernel.structs.metadata - Sample grexome0361 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.179 WARNING gcnvkernel.structs.metadata - Sample grexome0421 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.188 WARNING gcnvkernel.structs.metadata - Sample grexome0101 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.199 WARNING gcnvkernel.structs.metadata - Sample grexome0117 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.209 WARNING gcnvkernel.structs.metadata - Sample grexome0109 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.223 WARNING gcnvkernel.structs.metadata - Sample grexome0096 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.234 WARNING gcnvkernel.structs.metadata - Sample grexome0093 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.246 WARNING gcnvkernel.structs.metadata - Sample grexome0280 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.260 WARNING gcnvkernel.structs.metadata - Sample grexome0229 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.272 WARNING gcnvkernel.structs.metadata - Sample grexome0245 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designations. It is recommended that the user verifies this designation by orthogonal methods.
 06:00:35.282 WARNING gcnvkernel.structs.metadata - Sample grexome0372 has an anomalous karyotype ({'X': 2, 'Y': 1}). The presence of unmasked PAR regions and regions of low mappability in the coverage metadata can result in unreliable ploidy designat

 Stderr:
    at org.roadinstitute.hellbender.utils.python.PythonExecutorBase.getScriptException(PythonExecutorBase.java:75)
    at org.broadinstitute.hellbender.utils.runtime.ScriptExecutor.executeCuratedArgs(ScriptExecutor.java:126)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeArgs(PythonScriptExecutor.java:170)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:151)
    at org.broadinstitute.hellbender.utils.python.PythonScriptExecutor.executeScript(PythonScriptExecutor.java:121)
    at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.executeGermlineCNVCallerPythonScript(GermlineCNVCaller.java:454)
    at org.broadinstitute.hellbender.tools.copynumber.GermlineCNVCaller.doWork(GermlineCNVCaller.java:291)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
    at org.broadinstitute.hellbender.Main.main(Main.java:289)

is there a way to make the “anomalous karyotype” exception into a simple warning ? Otherwise I won't be able to complete a CNV calling with those samples.

Thank you.

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