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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.

Answers

  • lakhujanivijaylakhujanivijay IndiaMember

    Hi

    I am getting the same warning message while executing Germline Caller in cohort mode. Any clues what that could be ?

  • TintestTintest FranceMember

    Hello, by removing samples with Klinefelter Syndromes the tool manage to complete. I didn't find any other solution, sorry :'(

    Maybe if you could build your cohort with normal samples and then give specific ploidy to your problematic sample in SAMPLE mode, it could work :wink:

  • sleeslee Member, Broadie, Dev ✭✭✭

    @Tintest I believe that those warnings should not cause the tool to fail. Was there any additional output in the log (it looks like the text you copied might've gotten cut off)? Any chance you would be able to share your coverage files so that we can try to debug?

    @lakhujanivijay In general, you must be careful to blacklist problematic regions (as mentioned in the warning) in order to avoid misleading inferences on the sex chromosomes. As we've discussed elsewhere, making sure you recover correct results on a representative truth set is a good way to determine whether your blacklist is sufficient.

  • TintestTintest FranceMember

    Hello @slee, it was one year ago, unfortunately, I don't have the data anymore. Maybe the "stable" GCNV pipeline release should not fail with this kind of warning, but the beta did fail !

    If I'm working with infertile patients again, I'll try to come back and tell you, how is it going.

  • sleeslee Member, Broadie, Dev ✭✭✭

    Oops, sorry @Tintest, didn't realize the age of the original post---but thanks for your quick response! @lakhujanivijay if you are getting an actual tool failure (as opposed to just emitted warnings), please let us know.

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