Is there a better tool for visualizing your variants after annotation than Excel?
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6.7 years ago
Tania ▴ 180

Hi everyone

Is there a better tool for visualizing your variants after annotation using annovar or vep than excel, that also goes with git for version control? What do you use? Excel?

Thanks
annotations variants • 7.0k views
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2
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Define "visualizing" :)

As plain text/graphically ..

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I mean having a tabular view of your annotations so I can easily go through see what is interesting. The same way we do in Excel, but I don't like Excel for many reasons and looking to know what people use, if any better.

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You can try using a programmer's editor provided you are not saving your files in xlsx/xls format in first place. atom(PC/macOS), Notepad++(PC),BBEdit(macOS) are some of the options. Atom integrates with Git.

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If you are trying to use git or version control, consider saving your variant table in .tsv, .csv., .txt, or another raw text based format instead of .xlsx format. In theory this will allow better tracking of changes. Though in practice it becomes a moot point because often when the table changes, every line gets shifted such that entire file is considered 'changed' by git

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Thanks Steve. That would help, but I am looking for better tools than excel itself.

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1
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Excel is horrible, it will silently mutate your gene names. A good write-up here

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Amazing, thank you all :)

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3
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6.7 years ago

First, between annovar and vep I strongly prefer vep with vcf output format. Annovar's output looks good but I found its format to be quite inconsistent. Different fields have different information depending on the region being annotated and parsing it is quite messy (I don't have an example at hand now but I can find some).

Vep's vcf output instead looks ugly at first impression but is very consistent and simple to parse into something human readable. The annotation string in the CSQ tag is just a table with rows separated by , (I think) and columns separated by |, so if you are a bit familiar with command line tools like sed, bcftools etc it's easy to turn it into a simple table.

Having said that, at the cost of seeing my reputation dropping to -Inf, I think Excel is not too bad for eye-balling a table, provided your input is not too big. In fact, you could open the vcf file straightaway and with a couple of passes with Data -> Text to column... you could get something readable.

For some quick, geeky, searches through a possibly big but indexed vcf file the tool I have written, ASCIIGenome, has a print command. It gives a reasonably readable output and it has options to parse the printed output together with search & filter functions like find, grep, awk.
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6.7 years ago

I wrote vcf2table: it displays the VEP + SNPEFF(ANN=) annotations in a table. http://lindenb.github.io/jvarkit/VcfToTable.html

  VEP


+--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | PolyPhen                 | EXON | SIFT           | ALLELE_NUM | Gene            | SYMBOL | Protein_position | Consequence                                   | Amino_acids | Codons  | Feature         | BIOTYPE              |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+
 | probably_damaging(0.956) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 346/395          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000219240 | protein_coding       |
 |                          | 3/4  |                | 1          | ENSG00000102967 | DHODH  |                  | non_coding_exon_variant&nc_transcript_variant |             |         | ENST00000571392 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000572003 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573843 | retained_intron      |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  |                  | downstream_gene_variant                       |             |         | ENST00000573922 | processed_transcript |
 |                          |      |                | 1          | ENSG00000102967 | DHODH  | -/193            | intron_variant                                |             |         | ENST00000574309 | protein_coding       |
 | probably_damaging(0.946) | 8/9  | deleterious(0) | 1          | ENSG00000102967 | DHODH  | 344/393          | missense_variant                              | R/W         | Cgg/Tgg | ENST00000572887 | protein_coding       |
 +--------------------------+------+----------------+------------+-----------------+--------+------------------+-----------------------------------------------+-------------+---------+-----------------+----------------------+

one can filter the data upstream with snpsift of vcffilterso http://lindenb.github.io/jvarkit/VcfFilterSequenceOntology.html
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I get an error regarding the javac compiler when trying to install it:

~/jvarkit$ ./gradlew vcf2table
> Task :vcf2table FAILED

FAILURE: Build failed with an exception.

* Where:
Build file '/home/user/jvarkit/build.gradle' line: 681

* What went wrong:
Execution failed for vcf2table com.github.lindenb.jvarkit.tools.vcf2table.VcfToTable.
> Error running javac compiler

* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Get more help at https://help.gradle.org

BUILD FAILED in 686ms
1 actionable task: 1 executed

Java seems to be in the right location:

whereis java
java: /usr/bin/java /etc/java /usr/share/java /usr/share/man/man1/java.1.gz

$ echo $PATH
/home/user/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
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what is the version of java ? what is the value of ${JAVA_HOME} ?

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I actually did not have JAVA_HOME set up. After setting it up and adding it to PATH:

$ echo ${JAVA_HOME} 
/usr/lib/jvm/java-11-openjdk-amd64

$ echo $PATH 
/home/user/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/user/Bismark-0.22.3:/usr/lib/jvm/java-11-openjdk-amd64/bin

I still get the same error for the javac compiler. Regarding java version:

$ java --version
openjdk 11.0.16 2022-07-19
OpenJDK Runtime Environment (build 11.0.16+8-post-Ubuntu-0ubuntu120.04)
OpenJDK 64-Bit Server VM (build 11.0.16+8-post-Ubuntu-0ubuntu120.04, mixed mode, sharing)
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that's puzzling, it's the first time i see that error. Can you please retry with the --stacktrace option ? and show me the error trace.

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~/jvarkit$ ./gradlew --stacktrace vcf2table
> Task :vcf2table FAILED

FAILURE: Build failed with an exception.

* Where:
Build file '/home/user/jvarkit/build.gradle' line: 681

* What went wrong:
Execution failed for vcf2table com.github.lindenb.jvarkit.tools.vcf2table.VcfToTable.
> Error running javac compiler

* Try:
Run with --info or --debug option to get more log output. Run with --scan to get full insights.

* Exception is:
org.gradle.api.tasks.TaskExecutionException: Execution failed for vcf2table com.github.lindenb.jvarkit.tools.vcf2table.VcfToTable.
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.lambda$executeIfValid$1(ExecuteActionsTaskExecuter.java:200)
        at org.gradle.internal.Try$Failure.ifSuccessfulOrElse(Try.java:263)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:198)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:179)
        at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:109)
        at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:62)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:56)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:200)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:195)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:75)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:153)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:62)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.lambda$call$2(DefaultBuildOperationExecutor.java:76)
        at org.gradle.internal.operations.UnmanagedBuildOperationWrapper.callWithUnmanagedSupport(UnmanagedBuildOperationWrapper.java:54)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:76)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:41)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:372)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:359)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:352)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:338)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.lambda$run$0(DefaultPlanExecutor.java:127)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:191)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:182)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:124)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
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Caused by: : Error running javac compiler
        at org.apache.tools.ant.taskdefs.compilers.DefaultCompilerAdapter.executeExternalCompile(DefaultCompilerAdapter.java:591)
        at org.apache.tools.ant.taskdefs.compilers.JavacExternal.execute(JavacExternal.java:74)
        at org.apache.tools.ant.taskdefs.Javac.compile(Javac.java:1388)
        at org.apache.tools.ant.taskdefs.Javac.execute(Javac.java:1117)
        at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:99)
        at org.gradle.api.internal.project.ant.BasicAntBuilder.nodeCompleted(BasicAntBuilder.java:80)
        at org.gradle.api.internal.project.ant.BasicAntBuilder.doInvokeMethod(BasicAntBuilder.java:107)
        at CompileJVarkit.doIt(/home/user/jvarkit/build.gradle:681)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:104)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:58)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:51)
        at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:29)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$3.run(ExecuteActionsTaskExecuter.java:555)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:29)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$1.execute(DefaultBuildOperationRunner.java:26)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:75)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:153)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.run(DefaultBuildOperationRunner.java:56)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.lambda$run$1(DefaultBuildOperationExecutor.java:71)
        at org.gradle.internal.operations.UnmanagedBuildOperationWrapper.runWithUnmanagedSupport(UnmanagedBuildOperationWrapper.java:45)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:71)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:540)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:523)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.access$300(ExecuteActionsTaskExecuter.java:108)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.executeWithPreviousOutputFiles(ExecuteActionsTaskExecuter.java:271)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$TaskExecution.execute(ExecuteActionsTaskExecuter.java:260)
        at org.gradle.internal.execution.steps.ExecuteStep.lambda$execute$1(ExecuteStep.java:34)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:34)
        at org.gradle.internal.execution.steps.ExecuteStep.execute(ExecuteStep.java:26)
        at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:67)
        at org.gradle.internal.execution.steps.CleanupOutputsStep.execute(CleanupOutputsStep.java:36)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:49)
        at org.gradle.internal.execution.steps.ResolveInputChangesStep.execute(ResolveInputChangesStep.java:34)
        at org.gradle.internal.execution.steps.CancelExecutionStep.execute(CancelExecutionStep.java:43)
        at org.gradle.internal.execution.steps.TimeoutStep.executeWithoutTimeout(TimeoutStep.java:73)
        at org.gradle.internal.execution.steps.TimeoutStep.execute(TimeoutStep.java:54)
        at org.gradle.internal.execution.steps.CreateOutputsStep.execute(CreateOutputsStep.java:44)
        at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:54)
        at org.gradle.internal.execution.steps.SnapshotOutputsStep.execute(SnapshotOutputsStep.java:38)
        at org.gradle.internal.execution.steps.BroadcastChangingOutputsStep.execute(BroadcastChangingOutputsStep.java:42)
        at org.gradle.internal.execution.steps.CacheStep.executeWithoutCache(CacheStep.java:159)
        at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:72)
        at org.gradle.internal.execution.steps.CacheStep.execute(CacheStep.java:43)
        at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:44)
        at org.gradle.internal.execution.steps.StoreExecutionStateStep.execute(StoreExecutionStateStep.java:33)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:38)
        at org.gradle.internal.execution.steps.RecordOutputsStep.execute(RecordOutputsStep.java:24)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.executeBecause(SkipUpToDateStep.java:92)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.lambda$execute$0(SkipUpToDateStep.java:85)
        at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:55)
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 at org.gradle.internal.execution.steps.SkipUpToDateStep.execute(SkipUpToDateStep.java:39)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:76)
        at org.gradle.internal.execution.steps.ResolveChangesStep.execute(ResolveChangesStep.java:37)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:36)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsFinishedStep.execute(MarkSnapshottingInputsFinishedStep.java:26)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:94)
        at org.gradle.internal.execution.steps.ResolveCachingStateStep.execute(ResolveCachingStateStep.java:49)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:79)
        at org.gradle.internal.execution.steps.CaptureStateBeforeExecutionStep.execute(CaptureStateBeforeExecutionStep.java:53)
        at org.gradle.internal.execution.steps.ValidateStep.execute(ValidateStep.java:74)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.lambda$execute$2(SkipEmptyWorkStep.java:78)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:78)
        at org.gradle.internal.execution.steps.SkipEmptyWorkStep.execute(SkipEmptyWorkStep.java:34)
        at org.gradle.internal.execution.steps.legacy.MarkSnapshottingInputsStartedStep.execute(MarkSnapshottingInputsStartedStep.java:39)
        at org.gradle.internal.execution.steps.LoadExecutionStateStep.execute(LoadExecutionStateStep.java:40)
        at org.gradle.internal.execution.steps.LoadExecutionStateStep.execute(LoadExecutionStateStep.java:28)
        at org.gradle.internal.execution.impl.DefaultWorkExecutor.execute(DefaultWorkExecutor.java:33)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeIfValid(ExecuteActionsTaskExecuter.java:187)
        at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.execute(ExecuteActionsTaskExecuter.java:179)
        at org.gradle.api.internal.tasks.execution.CleanupStaleOutputsExecuter.execute(CleanupStaleOutputsExecuter.java:109)
        at org.gradle.api.internal.tasks.execution.FinalizePropertiesTaskExecuter.execute(FinalizePropertiesTaskExecuter.java:46)
        at org.gradle.api.internal.tasks.execution.ResolveTaskExecutionModeExecuter.execute(ResolveTaskExecutionModeExecuter.java:62)
        at org.gradle.api.internal.tasks.execution.SkipTaskWithNoActionsExecuter.execute(SkipTaskWithNoActionsExecuter.java:57)
        at org.gradle.api.internal.tasks.execution.SkipOnlyIfTaskExecuter.execute(SkipOnlyIfTaskExecuter.java:56)
        at org.gradle.api.internal.tasks.execution.CatchExceptionTaskExecuter.execute(CatchExceptionTaskExecuter.java:36)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.executeTask(EventFiringTaskExecuter.java:77)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:55)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter$1.call(EventFiringTaskExecuter.java:52)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:200)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$CallableBuildOperationWorker.execute(DefaultBuildOperationRunner.java:195)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:75)
        at org.gradle.internal.operations.DefaultBuildOperationRunner$3.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:153)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.execute(DefaultBuildOperationRunner.java:68)
        at org.gradle.internal.operations.DefaultBuildOperationRunner.call(DefaultBuildOperationRunner.java:62)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.lambda$call$2(DefaultBuildOperationExecutor.java:76)
        at org.gradle.internal.operations.UnmanagedBuildOperationWrapper.callWithUnmanagedSupport(UnmanagedBuildOperationWrapper.java:54)
        at org.gradle.internal.operations.DefaultBuildOperationExecutor.call(DefaultBuildOperationExecutor.java:76)
        at org.gradle.api.internal.tasks.execution.EventFiringTaskExecuter.execute(EventFiringTaskExecuter.java:52)
        at org.gradle.execution.plan.LocalTaskNodeExecutor.execute(LocalTaskNodeExecutor.java:41)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:372)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$InvokeNodeExecutorsAction.execute(DefaultTaskExecutionGraph.java:359)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:352)
        at org.gradle.execution.taskgraph.DefaultTaskExecutionGraph$BuildOperationAwareExecutionAction.execute(DefaultTaskExecutionGraph.java:338)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.lambda$run$0(DefaultPlanExecutor.java:127)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.execute(DefaultPlanExecutor.java:191)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.executeNextNode(DefaultPlanExecutor.java:182)
        at org.gradle.execution.plan.DefaultPlanExecutor$ExecutorWorker.run(DefaultPlanExecutor.java:124)
        at org.gradle.internal.concurrent.ExecutorPolicy$CatchAndRecordFailures.onExecute(ExecutorPolicy.java:64)
        at org.gradle.internal.concurrent.ManagedExecutorImpl$1.run(ManagedExecutorImpl.java:48)
        at org.gradle.internal.concurrent.ThreadFactoryImpl$ManagedThreadRunnable.run(ThreadFactoryImpl.java:56)
Caused by: java.io.IOException: Cannot run program "javac" (in directory "/home/user/jvarkit"): error=2, No such file or directory
        at org.apache.tools.ant.taskdefs.launcher.Java13CommandLauncher.exec(Java13CommandLauncher.java:58)
        at org.apache.tools.ant.taskdefs.Execute.launch(Execute.java:424)
        at org.apache.tools.ant.taskdefs.Execute.execute(Execute.java:438)
        at org.apache.tools.ant.taskdefs.compilers.DefaultCompilerAdapter.executeExternalCompile(DefaultCompilerAdapter.java:588)
        ... 109 more
Caused by: java.io.IOException: error=2, No such file or directory
        ... 113 more


* Get more help at https://help.gradle.org
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I must say that, for the sake of privacy, I have replaced the user name with 'user' in the code I paste here, but I trust it should not make any difference.

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thank you for the stacktrace; I'm puzzled. A few ideas. What's the output of

${JAVA_HOME}/bin/javac --version

?

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Caused by: java.io.IOException: Cannot run program "javac" (in directory "/home/user/jvarkit"): error=2, No such file or directory

hum... looks like it cannot find the right javac.

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Entering edit mode

Indeed it seems to be missing

 ${JAVA_HOME}/bin/javac --version
    bash: /usr/lib/jvm/java-11-openjdk-amd64/bin/javac: No such file or directory

So then should I just reinstall java?

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Yes, javac was missing for some reason, it works nicely after reinstalling jdk11. Thank you very much for the prompt responses!

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I got some warnings when trying to get the html version as indicated in Github:

$ java -jar ~/jvarkit/dist/vcf2table.jar multisample_selectvariants.vcf --color --format html > out.html
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by htsjdk.samtools.util.CloserUtil (file:/home/user/jvarkit/dist/vcf2table.jar) to method com.sun.xml.internal.stream.XMLEventReaderImpl.close()
WARNING: Please consider reporting this to the maintainers of htsjdk.samtools.util.CloserUtil
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release

Something to worry about?

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Something to worry about?

no

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6.7 years ago
Boris Shilov ▴ 10

If you use R, Rcommander works as a simple spreadsheet viewer pretty well, and readily integrates into your R workflow.
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6.6 years ago

In practice, something like this work quite ok for me, usually:

curl -s http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/functional_annotation/filtered/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.annotation.vcf.gz \
| bcftools query -f '%CHROM %POS %CSQ\n' \
| tr '|' ' ' \
| cut -d' ' -f 1-4,7 \
| grep 'UTR' \
| head \
| column -t

1  135000  A  ENSG00000237683  3_prime_UTR_variant
1  135030  G  ENSG00000237683  3_prime_UTR_variant
1  135031  T  ENSG00000237683  3_prime_UTR_variant
1  135094  T  ENSG00000237683  3_prime_UTR_variant
1  135095  T  ENSG00000237683  3_prime_UTR_variant
1  135135  T  ENSG00000237683  3_prime_UTR_variant
1  135151  A  ENSG00000237683  3_prime_UTR_variant
1  135162  A  ENSG00000237683  3_prime_UTR_variant
1  135163  T  ENSG00000237683  3_prime_UTR_variant
1  135173  A  ENSG00000237683  3_prime_UTR_variant

It may like horrible but it can go a long way to eyeball and look for something interesting...

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Entering edit mode
6.6 years ago

I pass them on to users in

a) JBrowse (as VCF, bgzipped and tabixed) to provide data integration with other information and genomic context and

b) as a table (usually VCF in libreoffice XLSX and or Galaxy)

c) but also sometimes use vcftotabular to create a nice but large TSVs from the VCF

Passing 8 million SNVs on isn't that clever, so I teach users to filter variants in Galaxy. I don't use git for version control of variants.

Certainly other visualization tools would be of interest.
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